Starting phenix.real_space_refine on Thu Dec 14 23:57:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq2_42458/12_2023/8uq2_42458_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.027 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 243": "OE1" <-> "OE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1194": "OD1" <-> "OD2" Residue "A PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1785": "OD1" <-> "OD2" Residue "A GLU 1891": "OE1" <-> "OE2" Residue "A PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A ASP 2482": "OD1" <-> "OD2" Residue "A ASP 2511": "OD1" <-> "OD2" Residue "A TYR 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3701": "OD1" <-> "OD2" Residue "A PHE 3714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3823": "OE1" <-> "OE2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4906": "OE1" <-> "OE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1194": "OD1" <-> "OD2" Residue "B PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1785": "OD1" <-> "OD2" Residue "B GLU 1891": "OE1" <-> "OE2" Residue "B PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2100": "NH1" <-> "NH2" Residue "B ASP 2482": "OD1" <-> "OD2" Residue "B ASP 2511": "OD1" <-> "OD2" Residue "B TYR 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3701": "OD1" <-> "OD2" Residue "B PHE 3714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3823": "OE1" <-> "OE2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4906": "OE1" <-> "OE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1131": "OD1" <-> "OD2" Residue "C PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1194": "OD1" <-> "OD2" Residue "C PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1785": "OD1" <-> "OD2" Residue "C GLU 1891": "OE1" <-> "OE2" Residue "C PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2100": "NH1" <-> "NH2" Residue "C ASP 2482": "OD1" <-> "OD2" Residue "C ASP 2511": "OD1" <-> "OD2" Residue "C TYR 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3701": "OD1" <-> "OD2" Residue "C PHE 3714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3823": "OE1" <-> "OE2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4906": "OE1" <-> "OE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1194": "OD1" <-> "OD2" Residue "D PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1785": "OD1" <-> "OD2" Residue "D GLU 1891": "OE1" <-> "OE2" Residue "D PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2100": "NH1" <-> "NH2" Residue "D ASP 2482": "OD1" <-> "OD2" Residue "D ASP 2511": "OD1" <-> "OD2" Residue "D TYR 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3701": "OD1" <-> "OD2" Residue "D PHE 3714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3823": "OE1" <-> "OE2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4906": "OE1" <-> "OE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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 180.021 179.491 87.942 1.00 74.01 S ATOM 33117 SG CYS A4891 179.974 181.976 90.808 1.00 72.77 S ATOM 70135 SG CYS B4888 205.682 180.009 87.969 1.00 73.51 S ATOM 70160 SG CYS B4891 203.199 179.963 90.837 1.00 72.41 S ATOM A030I SG CYS C4888 205.076 205.688 87.955 1.00 73.25 S ATOM A0317 SG CYS C4891 205.125 203.205 90.823 1.00 72.34 S ATOM A0T2L SG CYS D4888 179.406 205.085 87.970 1.00 73.53 S ATOM A0T3A SG CYS D4891 181.891 205.134 90.835 1.00 72.54 S Time building chain proxies: 95.21, per 1000 atoms: 0.69 Number of scatterers: 138608 At special positions: 0 Unit cell: (385.95, 385.95, 211.65, 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: 42.93 Conformation dependent library (CDL) restraints added in 34.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 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: 708 helices and 80 sheets defined 60.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 41.63 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.024A 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: 4.803A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.673A 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: 3.771A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.810A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.842A 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: 4.187A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 5.325A 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: 3.736A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.541A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.674A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.636A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.704A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.343A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.429A 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 857 through 862 removed outlier: 4.573A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 879 through 901 removed outlier: 4.672A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.091A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.875A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 5.291A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.570A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 5.053A 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: 3.528A pdb=" N LYS A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.437A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.893A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.660A 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 1230 through 1235 removed outlier: 7.137A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.925A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.110A 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 1494 Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.783A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.187A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.726A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.818A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.890A 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 1723 removed outlier: 4.661A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 5.711A pdb=" N THR A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.171A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.765A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.061A 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 1955 removed outlier: 4.302A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1967 removed outlier: 3.970A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 3.966A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.569A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.620A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) 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: 3.786A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.928A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.578A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.254A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.125A 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: 4.123A 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: 3.613A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.716A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) 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 2377 through 2382 removed outlier: 4.114A pdb=" N THR A2381 " --> pdb=" O GLU A2377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' 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: 5.572A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.675A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2510 removed outlier: 4.234A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2510' Processing helix chain 'A' and resid 2511 through 2532 removed outlier: 5.348A 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 2558 removed outlier: 4.328A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2581 removed outlier: 3.681A pdb=" N GLY A2578 " --> pdb=" O LEU A2574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A2581 " --> pdb=" O CYS A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2596 removed outlier: 4.088A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.615A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.119A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 removed outlier: 3.873A pdb=" N LEU A2666 " --> pdb=" O PHE A2662 " (cutoff:3.500A) Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2697 removed outlier: 3.729A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A2697 " --> pdb=" O SER A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.182A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS A2723 " --> pdb=" O TYR A2719 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A2724 " --> pdb=" O PHE A2720 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A2726 " --> pdb=" O ASN A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.568A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 4.467A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TRP A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.173A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.871A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2948 removed outlier: 3.561A pdb=" N SER A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.230A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.987A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 3.836A pdb=" N LEU A3061 " --> pdb=" O LEU A3057 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A3079 " --> pdb=" O LEU A3075 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.780A 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: 4.701A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3144 removed outlier: 6.697A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 3.634A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 removed outlier: 3.923A pdb=" N ALA A3160 " --> pdb=" O GLY A3156 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3177 removed outlier: 4.891A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3177' Processing helix chain 'A' and resid 3182 through 3188 removed outlier: 3.827A pdb=" N SER A3188 " --> pdb=" O TYR A3184 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 5.098A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 3.556A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) 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: 4.348A 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 3254 removed outlier: 5.728A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 5.261A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Proline residue: A3254 - end of helix Processing helix chain 'A' and resid 3269 through 3288 removed outlier: 3.503A pdb=" N ASN A3287 " --> pdb=" O ILE A3283 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A3288 " --> pdb=" O ILE A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.613A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.757A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3330 removed outlier: 5.211A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 3.625A pdb=" N LYS A3327 " --> pdb=" O MET A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3604 Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.624A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.292A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.910A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.696A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.867A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.893A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.863A 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: 4.569A 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 removed outlier: 3.858A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.966A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.628A 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 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.662A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.846A 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: 4.037A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 removed outlier: 4.566A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A4036 " --> pdb=" O PHE A4032 " (cutoff:3.500A) 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: 5.317A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.455A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.565A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (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 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4181 through 4207 removed outlier: 4.798A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4262 removed outlier: 4.448A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 removed outlier: 4.478A pdb=" N GLN A4267 " --> pdb=" O SER A4263 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.687A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 3.662A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 3.617A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A4518 " --> pdb=" O ASN A4514 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.447A 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: 3.710A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.262A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4701 removed outlier: 4.116A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.790A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.798A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.786A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.110A 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: 4.377A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.854A 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: 4.281A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.098A 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: 4.123A 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 915 through 920 removed outlier: 3.867A pdb=" N VAL A 919 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU A 920 " --> pdb=" O CYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 5.148A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2538 removed outlier: 4.111A pdb=" N GLY A2537 " --> pdb=" O LEU A2534 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A2538 " --> pdb=" O PHE A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.024A 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: 4.803A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.673A 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: 3.771A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.811A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.842A 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: 4.187A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 5.325A 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: 3.736A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.540A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.673A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.637A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.704A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.344A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.430A 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 857 through 862 removed outlier: 4.573A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 879 through 901 removed outlier: 4.672A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.091A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.875A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 5.290A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.571A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.053A 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: 3.527A pdb=" N LYS B 998 " --> pdb=" O ALA B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.438A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.893A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.660A 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 1230 through 1235 removed outlier: 7.137A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1230 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.925A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.110A 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 1494 Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.783A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.186A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.725A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.817A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.890A 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 1723 removed outlier: 4.660A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1737 removed outlier: 5.710A pdb=" N THR B1737 " --> pdb=" O THR B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.172A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.765A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.061A 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 1955 removed outlier: 4.303A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1967 removed outlier: 3.969A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 3.966A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.568A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.620A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) 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: 3.787A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.928A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.577A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.253A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.126A 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: 4.124A 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: 3.612A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.716A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) 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 2377 through 2382 removed outlier: 4.115A pdb=" N THR B2381 " --> pdb=" O GLU B2377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' 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: 5.572A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.676A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2510 removed outlier: 4.234A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2510' Processing helix chain 'B' and resid 2511 through 2532 removed outlier: 5.348A 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 2558 removed outlier: 4.327A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2581 removed outlier: 3.681A pdb=" N GLY B2578 " --> pdb=" O LEU B2574 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG B2581 " --> pdb=" O CYS B2577 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2596 removed outlier: 4.088A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.616A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.118A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 removed outlier: 3.872A pdb=" N LEU B2666 " --> pdb=" O PHE B2662 " (cutoff:3.500A) Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2697 removed outlier: 3.730A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B2697 " --> pdb=" O SER B2693 " (cutoff:3.500A) Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.182A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS B2723 " --> pdb=" O TYR B2719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B2724 " --> pdb=" O PHE B2720 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B2726 " --> pdb=" O ASN B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.568A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 4.467A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TRP B2773 " --> pdb=" O GLU B2769 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.173A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.871A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2948 removed outlier: 3.562A pdb=" N SER B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.230A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.986A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 3.836A pdb=" N LEU B3061 " --> pdb=" O LEU B3057 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN B3079 " --> pdb=" O LEU B3075 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.780A 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: 4.701A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3144 removed outlier: 6.696A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS B3144 " --> pdb=" O LEU B3140 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 3.635A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 removed outlier: 3.923A pdb=" N ALA B3160 " --> pdb=" O GLY B3156 " (cutoff:3.500A) Processing helix chain 'B' and resid 3172 through 3177 removed outlier: 4.892A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3177' Processing helix chain 'B' and resid 3182 through 3188 removed outlier: 3.827A pdb=" N SER B3188 " --> pdb=" O TYR B3184 " (cutoff:3.500A) Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 5.099A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 3.556A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) 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: 4.348A 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 3254 removed outlier: 5.728A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 5.260A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Proline residue: B3254 - end of helix Processing helix chain 'B' and resid 3269 through 3288 removed outlier: 3.503A pdb=" N ASN B3287 " --> pdb=" O ILE B3283 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B3288 " --> pdb=" O ILE B3284 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.612A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.757A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3330 removed outlier: 5.211A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 3.624A pdb=" N LYS B3327 " --> pdb=" O MET B3323 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3604 Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.623A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.292A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.911A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.696A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.867A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.893A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.864A 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: 4.569A 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 removed outlier: 3.859A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.967A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.629A 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 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.663A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.846A 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: 4.036A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 removed outlier: 4.567A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B4036 " --> pdb=" O PHE B4032 " (cutoff:3.500A) 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: 5.318A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.455A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.565A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (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 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4181 through 4207 removed outlier: 4.798A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4262 removed outlier: 4.449A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 removed outlier: 4.478A pdb=" N GLN B4267 " --> pdb=" O SER B4263 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.688A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 3.661A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 3.617A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B4518 " --> pdb=" O ASN B4514 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.447A 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: 3.711A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.262A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4701 removed outlier: 4.115A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.790A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.799A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.786A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.111A 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: 4.377A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.853A 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: 4.281A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.098A 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: 4.123A 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 915 through 920 removed outlier: 3.867A pdb=" N VAL B 919 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU B 920 " --> pdb=" O CYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 5.148A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 2533 through 2538 removed outlier: 4.111A pdb=" N GLY B2537 " --> pdb=" O LEU B2534 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B2538 " --> pdb=" O PHE B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.025A 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: 4.803A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.673A 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: 3.771A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.811A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.843A 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: 4.187A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 5.325A 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: 3.737A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 3.540A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 3.673A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 556 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.636A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.703A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.344A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.430A 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 857 through 862 removed outlier: 4.573A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 879 through 901 removed outlier: 4.672A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.091A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.874A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 5.291A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.571A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 5.053A 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: 3.528A pdb=" N LYS C 998 " --> pdb=" O ALA C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.437A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.893A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.660A 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 1230 through 1235 removed outlier: 7.136A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1230 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.924A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.109A 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 1494 Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.783A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.185A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.813A 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: 3.726A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.817A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.889A 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 1723 removed outlier: 4.659A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1737 removed outlier: 5.711A pdb=" N THR C1737 " --> pdb=" O THR C1733 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.171A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.765A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.061A 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 1955 removed outlier: 4.302A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1967 removed outlier: 3.969A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 3.966A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.568A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.620A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) 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: 3.787A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.928A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.578A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.253A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.125A 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: 4.123A 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: 3.612A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.716A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) 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 2377 through 2382 removed outlier: 4.114A pdb=" N THR C2381 " --> pdb=" O GLU C2377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' 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: 5.571A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.676A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2510 removed outlier: 4.234A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2510' Processing helix chain 'C' and resid 2511 through 2532 removed outlier: 5.349A 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 2558 removed outlier: 4.327A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2581 removed outlier: 3.680A pdb=" N GLY C2578 " --> pdb=" O LEU C2574 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG C2581 " --> pdb=" O CYS C2577 " (cutoff:3.500A) Processing helix chain 'C' and resid 2582 through 2596 removed outlier: 4.087A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.615A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.118A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 removed outlier: 3.872A pdb=" N LEU C2666 " --> pdb=" O PHE C2662 " (cutoff:3.500A) Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2697 removed outlier: 3.729A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C2697 " --> pdb=" O SER C2693 " (cutoff:3.500A) Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.182A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS C2723 " --> pdb=" O TYR C2719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR C2724 " --> pdb=" O PHE C2720 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU C2726 " --> pdb=" O ASN C2722 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.568A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 4.467A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TRP C2773 " --> pdb=" O GLU C2769 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.173A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.871A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2948 removed outlier: 3.562A pdb=" N SER C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.230A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.987A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 3.836A pdb=" N LEU C3061 " --> pdb=" O LEU C3057 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN C3079 " --> pdb=" O LEU C3075 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.779A 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: 4.701A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3144 removed outlier: 6.696A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 3.635A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 removed outlier: 3.923A pdb=" N ALA C3160 " --> pdb=" O GLY C3156 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3177 removed outlier: 4.892A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3177' Processing helix chain 'C' and resid 3182 through 3188 removed outlier: 3.828A pdb=" N SER C3188 " --> pdb=" O TYR C3184 " (cutoff:3.500A) Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 5.099A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 3.556A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) 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: 4.347A 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 3254 removed outlier: 5.727A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 5.261A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Proline residue: C3254 - end of helix Processing helix chain 'C' and resid 3269 through 3288 removed outlier: 3.503A pdb=" N ASN C3287 " --> pdb=" O ILE C3283 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C3288 " --> pdb=" O ILE C3284 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.613A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.756A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3330 removed outlier: 5.211A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 3.624A pdb=" N LYS C3327 " --> pdb=" O MET C3323 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3604 Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.623A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.292A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.912A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.696A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.867A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.893A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.863A 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: 4.569A 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 removed outlier: 3.858A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.967A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.628A 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 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.663A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.845A 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: 4.036A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 removed outlier: 4.567A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C4036 " --> pdb=" O PHE C4032 " (cutoff:3.500A) 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: 5.319A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.455A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.564A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (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 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4181 through 4207 removed outlier: 4.797A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4262 removed outlier: 4.449A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 removed outlier: 4.478A pdb=" N GLN C4267 " --> pdb=" O SER C4263 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.687A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 3.661A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 3.618A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C4518 " --> pdb=" O ASN C4514 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.448A 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: 3.711A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.262A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4701 removed outlier: 4.116A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.789A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.798A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.786A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.111A 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: 4.376A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.854A 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: 4.281A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.098A 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: 4.122A 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 915 through 920 removed outlier: 3.867A pdb=" N VAL C 919 " --> pdb=" O PRO C 916 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU C 920 " --> pdb=" O CYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 5.147A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 2533 through 2538 removed outlier: 4.110A pdb=" N GLY C2537 " --> pdb=" O LEU C2534 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR C2538 " --> pdb=" O PHE C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.024A 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: 4.804A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.673A 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: 3.772A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.810A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.842A 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: 4.187A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 5.325A 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: 3.736A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 3.541A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 3.673A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 556 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.636A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.704A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.343A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.430A 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 857 through 862 removed outlier: 4.574A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 879 through 901 removed outlier: 4.671A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.091A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.875A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 5.291A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.570A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 5.054A 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: 3.528A pdb=" N LYS D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.438A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.894A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.659A 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 1230 through 1235 removed outlier: 7.137A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1230 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.925A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.110A 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 1494 Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.783A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.185A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.725A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.817A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.889A 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 1723 removed outlier: 4.660A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1737 removed outlier: 5.711A pdb=" N THR D1737 " --> pdb=" O THR D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.171A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.765A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.061A 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 1955 removed outlier: 4.302A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1967 removed outlier: 3.971A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 3.965A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.568A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.621A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) 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: 3.786A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.929A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.578A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.254A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.126A 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: 4.123A 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: 3.612A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.716A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) 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 2377 through 2382 removed outlier: 4.113A pdb=" N THR D2381 " --> pdb=" O GLU D2377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' 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: 5.572A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.676A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2510 removed outlier: 4.235A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2510' Processing helix chain 'D' and resid 2511 through 2532 removed outlier: 5.348A 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 2558 removed outlier: 4.328A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2581 removed outlier: 3.682A pdb=" N GLY D2578 " --> pdb=" O LEU D2574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG D2581 " --> pdb=" O CYS D2577 " (cutoff:3.500A) Processing helix chain 'D' and resid 2582 through 2596 removed outlier: 4.088A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.615A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.119A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 removed outlier: 3.872A pdb=" N LEU D2666 " --> pdb=" O PHE D2662 " (cutoff:3.500A) Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2697 removed outlier: 3.729A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER D2697 " --> pdb=" O SER D2693 " (cutoff:3.500A) Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.181A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS D2723 " --> pdb=" O TYR D2719 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D2724 " --> pdb=" O PHE D2720 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU D2726 " --> pdb=" O ASN D2722 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.568A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 4.467A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TRP D2773 " --> pdb=" O GLU D2769 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.173A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.871A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2948 removed outlier: 3.562A pdb=" N SER D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.230A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.987A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 3.835A pdb=" N LEU D3061 " --> pdb=" O LEU D3057 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN D3079 " --> pdb=" O LEU D3075 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.780A 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: 4.701A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3144 removed outlier: 6.697A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS D3144 " --> pdb=" O LEU D3140 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 3.634A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 removed outlier: 3.922A pdb=" N ALA D3160 " --> pdb=" O GLY D3156 " (cutoff:3.500A) Processing helix chain 'D' and resid 3172 through 3177 removed outlier: 4.892A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3177' Processing helix chain 'D' and resid 3182 through 3188 removed outlier: 3.828A pdb=" N SER D3188 " --> pdb=" O TYR D3184 " (cutoff:3.500A) Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 5.099A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 3.557A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) 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: 4.348A 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 3254 removed outlier: 5.728A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 5.261A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Proline residue: D3254 - end of helix Processing helix chain 'D' and resid 3269 through 3288 removed outlier: 3.503A pdb=" N ASN D3287 " --> pdb=" O ILE D3283 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU D3288 " --> pdb=" O ILE D3284 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.613A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.757A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3330 removed outlier: 5.211A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 3.623A pdb=" N LYS D3327 " --> pdb=" O MET D3323 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3604 Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.624A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.293A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.910A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.696A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.867A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.893A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.863A 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: 4.570A 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 removed outlier: 3.858A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.967A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.629A 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 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.663A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.844A 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: 4.037A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 removed outlier: 4.567A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP D4036 " --> pdb=" O PHE D4032 " (cutoff:3.500A) 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: 5.317A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.455A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.565A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (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 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4181 through 4207 removed outlier: 4.798A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4262 removed outlier: 4.449A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 removed outlier: 4.478A pdb=" N GLN D4267 " --> pdb=" O SER D4263 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.687A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 3.661A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 3.617A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D4518 " --> pdb=" O ASN D4514 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.448A 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: 3.711A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.261A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4701 removed outlier: 4.116A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.790A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.798A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.785A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.110A 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: 4.376A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.853A 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: 4.280A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.097A 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: 4.122A 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 915 through 920 removed outlier: 3.866A pdb=" N VAL D 919 " --> pdb=" O PRO D 916 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU D 920 " --> pdb=" O CYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 5.148A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 2533 through 2538 removed outlier: 4.111A pdb=" N GLY D2537 " --> pdb=" O LEU D2534 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR D2538 " --> pdb=" O PHE D2535 " (cutoff:3.500A) 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: 5.129A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.947A 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: 5.128A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.947A 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: 5.128A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.947A 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: 5.129A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.948A 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 52 removed outlier: 6.253A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.190A 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: 6.657A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (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 removed outlier: 3.774A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= 6, first strand: chain 'A' and resid 303 through 306 removed outlier: 3.602A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.635A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.857A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.415A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= 13, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 6.891A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.789A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.708A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 4.760A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2742 through 2745 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 19, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.590A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.253A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.189A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.658A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 23, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.774A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= 25, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.602A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 27, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.635A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.857A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 30, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.415A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1016 through 1019 Processing sheet with id= 32, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 6.891A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.790A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.708A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 4.760A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 2742 through 2745 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 38, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.590A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.253A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.190A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.657A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 42, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.774A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= 44, first strand: chain 'C' and resid 303 through 306 removed outlier: 3.602A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 46, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.635A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.858A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 49, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.415A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1016 through 1019 Processing sheet with id= 51, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 6.892A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.790A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.709A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 4.760A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 2742 through 2745 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 57, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.590A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.253A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.189A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.658A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 61, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.774A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 243 through 247 Processing sheet with id= 63, first strand: chain 'D' and resid 303 through 306 removed outlier: 3.602A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 65, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.636A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.858A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 68, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.416A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 1016 through 1019 Processing sheet with id= 70, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 6.891A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.790A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.707A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 4.760A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 2742 through 2745 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 76, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.590A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'E' and resid 3 through 8 removed outlier: 4.020A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 3 through 8 removed outlier: 4.019A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'G' and resid 3 through 8 removed outlier: 4.019A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 3 through 8 removed outlier: 4.020A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 7352 hydrogen bonds defined for protein. 21932 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: 103.36 Time building geometry restraints manager: 46.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 24498 1.32 - 1.45: 36439 1.45 - 1.57: 79135 1.57 - 1.70: 44 1.70 - 1.82: 1512 Bond restraints: 141628 Sorted by residual: bond pdb=" C VAL B2596 " pdb=" N PRO B2597 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.55e+00 bond pdb=" C VAL C2596 " pdb=" N PRO C2597 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.52e+00 bond pdb=" C VAL D2596 " pdb=" N PRO D2597 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.45e+00 bond pdb=" CB GLU F 4 " pdb=" CG GLU F 4 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" C VAL A2596 " pdb=" N PRO A2597 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.27e+00 ... (remaining 141623 not shown) Histogram of bond angle deviations from ideal: 95.88 - 104.68: 2593 104.68 - 113.47: 77791 113.47 - 122.27: 90219 122.27 - 131.07: 20042 131.07 - 139.86: 711 Bond angle restraints: 191356 Sorted by residual: angle pdb=" C PRO A 705 " pdb=" N TYR A 706 " pdb=" CA TYR A 706 " ideal model delta sigma weight residual 121.17 132.09 -10.92 1.62e+00 3.81e-01 4.54e+01 angle pdb=" C PRO D 705 " pdb=" N TYR D 706 " pdb=" CA TYR D 706 " ideal model delta sigma weight residual 121.17 132.05 -10.88 1.62e+00 3.81e-01 4.51e+01 angle pdb=" C PRO C 705 " pdb=" N TYR C 706 " pdb=" CA TYR C 706 " ideal model delta sigma weight residual 121.17 132.03 -10.86 1.62e+00 3.81e-01 4.50e+01 angle pdb=" C PRO B 705 " pdb=" N TYR B 706 " pdb=" CA TYR B 706 " ideal model delta sigma weight residual 121.17 132.00 -10.83 1.62e+00 3.81e-01 4.47e+01 angle pdb=" CA GLN A2928 " pdb=" CB GLN A2928 " pdb=" CG GLN A2928 " ideal model delta sigma weight residual 114.10 127.15 -13.05 2.00e+00 2.50e-01 4.26e+01 ... (remaining 191351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 77391 17.91 - 35.81: 6413 35.81 - 53.72: 1131 53.72 - 71.62: 393 71.62 - 89.53: 84 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 -137.25 -42.75 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -137.25 -42.75 0 5.00e+00 4.00e-02 7.31e+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 -137.27 -42.73 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 85409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 20062 0.093 - 0.186: 882 0.186 - 0.278: 40 0.278 - 0.371: 0 0.371 - 0.464: 4 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CG LEU D2929 " pdb=" CB LEU D2929 " pdb=" CD1 LEU D2929 " pdb=" CD2 LEU D2929 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CG LEU B2929 " pdb=" CB LEU B2929 " pdb=" CD1 LEU B2929 " pdb=" CD2 LEU B2929 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CG LEU C2929 " pdb=" CB LEU C2929 " pdb=" CD1 LEU C2929 " pdb=" CD2 LEU C2929 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " 0.102 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO B4641 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.102 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO C4641 " -0.271 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.102 5.00e-02 4.00e+02 1.57e-01 3.93e+01 pdb=" N PRO A4641 " -0.271 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.080 5.00e-02 4.00e+02 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1630 2.64 - 3.20: 130764 3.20 - 3.77: 229356 3.77 - 4.33: 313207 4.33 - 4.90: 503211 Nonbonded interactions: 1178168 Sorted by model distance: nonbonded pdb=" OG SER C2764 " pdb=" OE1 GLU C2767 " model vdw 2.072 2.440 nonbonded pdb=" OG SER A2764 " pdb=" OE1 GLU A2767 " model vdw 2.072 2.440 nonbonded pdb=" OG SER D2764 " pdb=" OE1 GLU D2767 " model vdw 2.073 2.440 nonbonded pdb=" OG SER B2764 " pdb=" OE1 GLU B2767 " model vdw 2.073 2.440 nonbonded pdb=" O TYR A3184 " pdb=" NH2 ARG A3192 " model vdw 2.084 2.520 ... (remaining 1178163 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 31.030 Check model and map are aligned: 1.500 Set scattering table: 1.030 Process input model: 450.900 Find NCS groups from input model: 7.820 Set up NCS constraints: 1.130 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: 0.040 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 511.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.054 141628 Z= 0.199 Angle : 0.746 13.595 191356 Z= 0.417 Chirality : 0.042 0.464 20988 Planarity : 0.006 0.157 24588 Dihedral : 14.079 89.530 52936 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 0.50 % Allowed : 0.52 % Favored : 98.98 % 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: 0.81 (0.06), residues: 17212 helix: 1.25 (0.06), residues: 9044 sheet: 0.43 (0.14), residues: 1532 loop : -0.33 (0.08), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D3250 HIS 0.015 0.001 HIS B3700 PHE 0.061 0.002 PHE B2925 TYR 0.045 0.002 TYR B2939 ARG 0.018 0.001 ARG D 913 *********************** 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 1361 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1285 time to evaluate : 12.109 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 outliers start: 76 outliers final: 22 residues processed: 1308 average time/residue: 2.0838 time to fit residues: 3912.9756 Evaluate side-chains 1115 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1093 time to evaluate : 11.759 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 7 residues processed: 22 average time/residue: 2.5047 time to fit residues: 89.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 6.9990 chunk 1309 optimal weight: 7.9990 chunk 726 optimal weight: 6.9990 chunk 447 optimal weight: 10.0000 chunk 883 optimal weight: 2.9990 chunk 699 optimal weight: 8.9990 chunk 1354 optimal weight: 5.9990 chunk 524 optimal weight: 9.9990 chunk 823 optimal weight: 7.9990 chunk 1008 optimal weight: 10.0000 chunk 1569 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1995 GLN ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1995 GLN ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 GLN ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS D 949 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1995 GLN ** D2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 141628 Z= 0.422 Angle : 0.727 14.325 191356 Z= 0.364 Chirality : 0.045 0.224 20988 Planarity : 0.006 0.144 24588 Dihedral : 5.913 86.858 19028 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 0.57 % Allowed : 6.24 % Favored : 93.20 % 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: 0.93 (0.06), residues: 17212 helix: 1.38 (0.06), residues: 9128 sheet: 0.42 (0.13), residues: 1580 loop : -0.35 (0.08), residues: 6504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D3249 HIS 0.014 0.002 HIS B3700 PHE 0.033 0.002 PHE D2925 TYR 0.043 0.002 TYR A3131 ARG 0.011 0.001 ARG A3152 *********************** 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 1302 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1216 time to evaluate : 11.947 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 outliers start: 86 outliers final: 23 residues processed: 1229 average time/residue: 2.1799 time to fit residues: 3894.4235 Evaluate side-chains 1146 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1123 time to evaluate : 11.933 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 10 residues processed: 21 average time/residue: 1.5810 time to fit residues: 68.8658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.9980 chunk 487 optimal weight: 8.9990 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 8.9990 chunk 432 optimal weight: 5.9990 chunk 1572 optimal weight: 40.0000 chunk 1698 optimal weight: 10.0000 chunk 1400 optimal weight: 9.9990 chunk 1558 optimal weight: 8.9990 chunk 535 optimal weight: 0.5980 chunk 1261 optimal weight: 10.0000 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN A 635 ASN A 651 HIS ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2802 ASN A2978 HIS ** A3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3901 GLN ** A4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN H 32 GLN ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2802 ASN ** B2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2802 ASN C2937 HIS ** C2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN D 651 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2802 ASN ** D2978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 141628 Z= 0.410 Angle : 0.709 16.219 191356 Z= 0.352 Chirality : 0.044 0.202 20988 Planarity : 0.005 0.138 24588 Dihedral : 5.767 78.338 19028 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 0.55 % Allowed : 7.88 % Favored : 91.58 % 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: 1.01 (0.06), residues: 17212 helix: 1.47 (0.05), residues: 9112 sheet: 0.33 (0.13), residues: 1552 loop : -0.30 (0.08), residues: 6548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A3250 HIS 0.013 0.001 HIS B3700 PHE 0.046 0.002 PHE D3302 TYR 0.060 0.002 TYR D2939 ARG 0.015 0.001 ARG A2258 *********************** 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 1280 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1197 time to evaluate : 10.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 16 residues processed: 1206 average time/residue: 2.1339 time to fit residues: 3797.4495 Evaluate side-chains 1129 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1113 time to evaluate : 11.985 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 6 residues processed: 13 average time/residue: 1.6969 time to fit residues: 51.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 9.9990 chunk 1181 optimal weight: 20.0000 chunk 815 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 750 optimal weight: 20.0000 chunk 1055 optimal weight: 0.0980 chunk 1577 optimal weight: 30.0000 chunk 1670 optimal weight: 1.9990 chunk 824 optimal weight: 0.0770 chunk 1495 optimal weight: 2.9990 chunk 450 optimal weight: 7.9990 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2587 HIS ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2978 HIS ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3901 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2978 HIS ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3901 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2654 GLN ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2937 HIS D2978 HIS ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 141628 Z= 0.224 Angle : 0.688 17.642 191356 Z= 0.336 Chirality : 0.042 0.261 20988 Planarity : 0.005 0.132 24588 Dihedral : 5.632 77.450 19028 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 0.72 % Allowed : 8.82 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % 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: 1.10 (0.07), residues: 17212 helix: 1.58 (0.06), residues: 9104 sheet: 0.38 (0.14), residues: 1492 loop : -0.32 (0.08), residues: 6616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A3249 HIS 0.013 0.001 HIS A3700 PHE 0.028 0.001 PHE D1942 TYR 0.055 0.001 TYR A2939 ARG 0.016 0.000 ARG D2258 *********************** 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 1276 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1167 time to evaluate : 12.117 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 outliers start: 109 outliers final: 20 residues processed: 1206 average time/residue: 2.1473 time to fit residues: 3788.5277 Evaluate side-chains 1133 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1113 time to evaluate : 12.026 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 7 residues processed: 13 average time/residue: 1.6382 time to fit residues: 51.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 1.9990 chunk 948 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 1243 optimal weight: 8.9990 chunk 689 optimal weight: 10.0000 chunk 1425 optimal weight: 0.1980 chunk 1154 optimal weight: 40.0000 chunk 1 optimal weight: 0.9980 chunk 852 optimal weight: 0.9990 chunk 1499 optimal weight: 10.0000 chunk 421 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1974 ASN ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1974 ASN ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3806 ASN ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2847 ASN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 141628 Z= 0.206 Angle : 0.695 18.575 191356 Z= 0.336 Chirality : 0.041 0.276 20988 Planarity : 0.005 0.162 24588 Dihedral : 5.512 77.212 19028 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 0.67 % Allowed : 9.59 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % 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: 1.16 (0.07), residues: 17212 helix: 1.63 (0.06), residues: 9100 sheet: 0.37 (0.14), residues: 1528 loop : -0.27 (0.08), residues: 6584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A3249 HIS 0.012 0.001 HIS A3700 PHE 0.050 0.001 PHE D3302 TYR 0.065 0.001 TYR D2939 ARG 0.018 0.000 ARG B2258 *********************** 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 1274 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1172 time to evaluate : 12.027 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 outliers start: 102 outliers final: 23 residues processed: 1214 average time/residue: 2.0730 time to fit residues: 3675.2419 Evaluate side-chains 1144 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1121 time to evaluate : 10.706 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 13 residues processed: 12 average time/residue: 1.3372 time to fit residues: 40.8763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 330 optimal weight: 8.9990 chunk 980 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 1671 optimal weight: 4.9990 chunk 1387 optimal weight: 10.0000 chunk 774 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 553 optimal weight: 5.9990 chunk 877 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 635 ASN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS C 587 ASN C 635 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 ASN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 141628 Z= 0.490 Angle : 0.764 17.828 191356 Z= 0.374 Chirality : 0.045 0.280 20988 Planarity : 0.005 0.152 24588 Dihedral : 5.535 77.909 19028 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 0.72 % Allowed : 10.38 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.07), residues: 17212 helix: 1.56 (0.06), residues: 9084 sheet: 0.23 (0.14), residues: 1516 loop : -0.30 (0.08), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C3249 HIS 0.011 0.001 HIS B3732 PHE 0.032 0.002 PHE B3117 TYR 0.049 0.002 TYR B 931 ARG 0.017 0.001 ARG B2886 *********************** 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 1280 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1170 time to evaluate : 11.970 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 outliers start: 110 outliers final: 26 residues processed: 1202 average time/residue: 2.1250 time to fit residues: 3744.2348 Evaluate side-chains 1149 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1123 time to evaluate : 11.886 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 14 residues processed: 14 average time/residue: 1.3985 time to fit residues: 49.4216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 952 optimal weight: 3.9990 chunk 1220 optimal weight: 0.8980 chunk 945 optimal weight: 2.9990 chunk 1407 optimal weight: 30.0000 chunk 933 optimal weight: 5.9990 chunk 1665 optimal weight: 2.9990 chunk 1042 optimal weight: 0.8980 chunk 1015 optimal weight: 0.9990 chunk 768 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2654 GLN ** A2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4558 HIS B 587 ASN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2654 GLN ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2847 ASN ** B2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3256 ASN ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS C 587 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2654 GLN ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS D 587 ASN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2899 ASN ** D2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3256 ASN ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 141628 Z= 0.194 Angle : 0.735 18.440 191356 Z= 0.351 Chirality : 0.042 0.345 20988 Planarity : 0.005 0.141 24588 Dihedral : 5.406 82.975 19028 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.55 % Allowed : 10.95 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % 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: 1.14 (0.07), residues: 17212 helix: 1.62 (0.06), residues: 9108 sheet: 0.30 (0.14), residues: 1512 loop : -0.29 (0.08), residues: 6592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C4481 HIS 0.013 0.001 HIS A3700 PHE 0.054 0.001 PHE A3302 TYR 0.059 0.001 TYR D2939 ARG 0.018 0.000 ARG B2772 *********************** 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 1255 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1172 time to evaluate : 11.947 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 outliers start: 83 outliers final: 25 residues processed: 1204 average time/residue: 2.0639 time to fit residues: 3652.4499 Evaluate side-chains 1126 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1101 time to evaluate : 12.023 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 1.7787 time to fit residues: 27.8646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 3.9990 chunk 665 optimal weight: 4.9990 chunk 994 optimal weight: 2.9990 chunk 501 optimal weight: 20.0000 chunk 327 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 1058 optimal weight: 7.9990 chunk 1134 optimal weight: 9.9990 chunk 823 optimal weight: 7.9990 chunk 155 optimal weight: 0.0570 chunk 1309 optimal weight: 8.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2838 HIS B ** A2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4558 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2847 ASN ** C2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2847 ASN ** D2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3806 ASN ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 141628 Z= 0.229 Angle : 0.752 20.631 191356 Z= 0.359 Chirality : 0.043 0.349 20988 Planarity : 0.005 0.136 24588 Dihedral : 5.304 89.743 19028 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 0.44 % Allowed : 11.62 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % 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: 1.17 (0.07), residues: 17212 helix: 1.62 (0.06), residues: 9140 sheet: 0.39 (0.14), residues: 1480 loop : -0.27 (0.08), residues: 6592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A4481 HIS 0.014 0.001 HIS D4055 PHE 0.040 0.001 PHE C3022 TYR 0.058 0.001 TYR B2939 ARG 0.019 0.000 ARG B2772 *********************** 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 1210 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1143 time to evaluate : 11.861 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 outliers start: 67 outliers final: 27 residues processed: 1175 average time/residue: 2.1395 time to fit residues: 3674.0281 Evaluate side-chains 1124 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1097 time to evaluate : 11.844 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 7 average time/residue: 1.2618 time to fit residues: 31.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 0.2980 chunk 1595 optimal weight: 5.9990 chunk 1455 optimal weight: 9.9990 chunk 1552 optimal weight: 10.0000 chunk 934 optimal weight: 7.9990 chunk 676 optimal weight: 0.0370 chunk 1218 optimal weight: 7.9990 chunk 476 optimal weight: 3.9990 chunk 1402 optimal weight: 20.0000 chunk 1467 optimal weight: 0.9990 chunk 1546 optimal weight: 7.9990 overall best weight: 2.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3806 ASN ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4558 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2995 HIS ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2995 HIS ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2847 ASN ** D2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 141628 Z= 0.242 Angle : 0.770 18.055 191356 Z= 0.368 Chirality : 0.043 0.358 20988 Planarity : 0.004 0.081 24588 Dihedral : 5.258 87.004 19028 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 0.34 % Allowed : 11.99 % Favored : 87.66 % Cbeta Deviations : 0.01 % 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: 1.19 (0.07), residues: 17212 helix: 1.65 (0.06), residues: 9076 sheet: 0.37 (0.14), residues: 1488 loop : -0.25 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D3249 HIS 0.014 0.001 HIS B2541 PHE 0.054 0.002 PHE B2975 TYR 0.057 0.001 TYR D2939 ARG 0.023 0.000 ARG D2772 *********************** 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 1185 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1133 time to evaluate : 12.254 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 outliers start: 52 outliers final: 24 residues processed: 1163 average time/residue: 2.2035 time to fit residues: 3739.6906 Evaluate side-chains 1127 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1103 time to evaluate : 10.641 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 1.7886 time to fit residues: 32.7868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 7.9990 chunk 1641 optimal weight: 0.9990 chunk 1001 optimal weight: 10.0000 chunk 778 optimal weight: 9.9990 chunk 1140 optimal weight: 30.0000 chunk 1721 optimal weight: 1.9990 chunk 1584 optimal weight: 10.0000 chunk 1370 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 1058 optimal weight: 7.9990 chunk 840 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 HIS ** A2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4558 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3806 ASN ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2838 HIS A ** C2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2995 HIS ** D3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 141628 Z= 0.320 Angle : 0.796 20.578 191356 Z= 0.382 Chirality : 0.044 0.368 20988 Planarity : 0.005 0.082 24588 Dihedral : 5.228 80.317 19028 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 0.25 % Allowed : 12.15 % Favored : 87.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.01 % 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: 1.13 (0.07), residues: 17212 helix: 1.61 (0.06), residues: 9092 sheet: 0.39 (0.14), residues: 1472 loop : -0.29 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D3249 HIS 0.011 0.001 HIS A3700 PHE 0.086 0.002 PHE B2975 TYR 0.054 0.002 TYR B2939 ARG 0.019 0.001 ARG D1960 ********************** 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 1171 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1133 time to evaluate : 11.387 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 outliers start: 38 outliers final: 25 residues processed: 1158 average time/residue: 2.1493 time to fit residues: 3651.5809 Evaluate side-chains 1135 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1110 time to evaluate : 11.932 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 5 average time/residue: 1.3493 time to fit residues: 28.1431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 3.9990 chunk 1460 optimal weight: 5.9990 chunk 419 optimal weight: 6.9990 chunk 1264 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 380 optimal weight: 4.9990 chunk 1373 optimal weight: 8.9990 chunk 574 optimal weight: 10.0000 chunk 1409 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 HIS A2995 HIS ** A3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4558 HIS ** B 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2838 HIS A C2995 HIS ** C3095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3256 ASN ** C3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4558 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2995 HIS ** D3811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.053247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.037544 restraints weight = 976985.807| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.71 r_work: 0.2756 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 141628 Z= 0.259 Angle : 0.800 20.077 191356 Z= 0.383 Chirality : 0.044 0.384 20988 Planarity : 0.005 0.082 24588 Dihedral : 5.162 74.548 19028 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 0.28 % Allowed : 12.26 % Favored : 87.46 % Cbeta Deviations : 0.02 % 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: 1.12 (0.07), residues: 17212 helix: 1.59 (0.06), residues: 9092 sheet: 0.39 (0.14), residues: 1472 loop : -0.29 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D3249 HIS 0.033 0.001 HIS C3233 PHE 0.094 0.002 PHE B2975 TYR 0.058 0.001 TYR D2939 ARG 0.018 0.000 ARG D2772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54711.74 seconds wall clock time: 954 minutes 57.24 seconds (57297.24 seconds total)