Starting phenix.real_space_refine on Mon Mar 18 21:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9q_26405/03_2024/7u9q_26405_updated.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.028 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 "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1741": "OD1" <-> "OD2" Residue "A ASP 2261": "OD1" <-> "OD2" Residue "A TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2944": "OD1" <-> "OD2" Residue "A GLU 2952": "OE1" <-> "OE2" Residue "A ARG 3058": "NH1" <-> "NH2" Residue "A TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3632": "OE1" <-> "OE2" Residue "A PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4182": "OE1" <-> "OE2" Residue "A ASP 4278": "OD1" <-> "OD2" Residue "A PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4624": "OD1" <-> "OD2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D ASP 641": "OD1" <-> "OD2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1009": "NH1" <-> "NH2" Residue "D ARG 1013": "NH1" <-> "NH2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1741": "OD1" <-> "OD2" Residue "D ASP 2261": "OD1" <-> "OD2" Residue "D TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2944": "OD1" <-> "OD2" Residue "D GLU 2952": "OE1" <-> "OE2" Residue "D ARG 3058": "NH1" <-> "NH2" Residue "D TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3632": "OE1" <-> "OE2" Residue "D PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4182": "OE1" <-> "OE2" Residue "D ASP 4278": "OD1" <-> "OD2" Residue "D PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4624": "OD1" <-> "OD2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B ASP 641": "OD1" <-> "OD2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1009": "NH1" <-> "NH2" Residue "B ARG 1013": "NH1" <-> "NH2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1741": "OD1" <-> "OD2" Residue "B ASP 2261": "OD1" <-> "OD2" Residue "B TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2944": "OD1" <-> "OD2" Residue "B GLU 2952": "OE1" <-> "OE2" Residue "B ARG 3058": "NH1" <-> "NH2" Residue "B TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3632": "OE1" <-> "OE2" Residue "B PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4182": "OE1" <-> "OE2" Residue "B ASP 4278": "OD1" <-> "OD2" Residue "B PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4624": "OD1" <-> "OD2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C ASP 641": "OD1" <-> "OD2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1009": "NH1" <-> "NH2" Residue "C ARG 1013": "NH1" <-> "NH2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1741": "OD1" <-> "OD2" Residue "C ASP 2261": "OD1" <-> "OD2" Residue "C TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2944": "OD1" <-> "OD2" Residue "C GLU 2952": "OE1" <-> "OE2" Residue "C ARG 3058": "NH1" <-> "NH2" Residue "C TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3632": "OE1" <-> "OE2" Residue "C PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4182": "OE1" <-> "OE2" Residue "C ASP 4278": "OD1" <-> "OD2" Residue "C PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4624": "OD1" <-> "OD2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138608 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "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: "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: "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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33910 SG CYS A4888 179.383 203.079 124.767 1.00 70.69 S ATOM 33935 SG CYS A4891 178.214 200.671 122.034 1.00 68.80 S ATOM 70135 SG CYS D4888 169.765 179.327 124.969 1.00 71.73 S ATOM 70160 SG CYS D4891 172.181 178.152 122.245 1.00 69.33 S ATOM A030I SG CYS B4888 203.228 193.745 124.771 1.00 70.63 S ATOM A0317 SG CYS B4891 200.820 194.912 122.037 1.00 69.63 S ATOM A0T2L SG CYS C4888 193.700 169.893 124.781 1.00 69.80 S ATOM A0T3A SG CYS C4891 194.865 172.299 122.045 1.00 68.42 S Time building chain proxies: 97.66, per 1000 atoms: 0.70 Number of scatterers: 138608 At special positions: 0 Unit cell: (373.568, 373.568, 212.992, 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 D4806 " - pdb=" SG CYS D4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.04 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.04 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: 42.60 Conformation dependent library (CDL) restraints added in 36.5 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: 696 helices and 80 sheets defined 59.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 44.74 Creating SS restraints... Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.579A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.161A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.097A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.579A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.160A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.097A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.579A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.161A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.098A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.579A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.161A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.097A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.931A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 219 through 224 removed outlier: 5.719A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.683A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.736A pdb=" N HIS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.610A pdb=" N ARG A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.970A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 4.364A pdb=" N VAL A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 493 removed outlier: 3.528A pdb=" N GLU A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.607A pdb=" N VAL A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.634A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.726A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.545A pdb=" N PHE A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.138A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.586A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 4.242A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 590' Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.535A pdb=" N SER A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.832A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.576A pdb=" N ILE A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.592A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.767A 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 875 through 901 removed outlier: 4.035A pdb=" N ILE A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 removed outlier: 3.944A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix No H-bonds generated for 'chain 'A' and resid 920 through 925' Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 954 through 960 Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.967A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.788A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.359A 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: 7.153A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.878A 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 removed outlier: 4.181A pdb=" N MET A1421 " --> pdb=" O TYR A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.420A 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: 3.833A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.308A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.823A 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: 3.766A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.645A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A1677 " --> pdb=" O ALA A1673 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 3.612A pdb=" N ALA A1688 " --> pdb=" O GLN A1684 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1710 removed outlier: 3.540A pdb=" N TYR A1703 " --> pdb=" O ARG A1699 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A1706 " --> pdb=" O TYR A1702 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A1707 " --> pdb=" O TYR A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.158A pdb=" N ALA A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A1716 " --> pdb=" O SER A1712 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A1717 " --> pdb=" O SER A1713 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A1719 " --> pdb=" O ALA A1715 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 4.293A pdb=" N SER A1735 " --> pdb=" O GLU A1731 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 removed outlier: 3.625A pdb=" N LEU A1787 " --> pdb=" O PRO A1783 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A1788 " --> pdb=" O LEU A1784 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A1789 " --> pdb=" O ASP A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 removed outlier: 3.693A pdb=" N VAL A1819 " --> pdb=" O GLU A1815 " (cutoff:3.500A) Proline residue: A1820 - end of helix removed outlier: 3.789A pdb=" N LYS A1823 " --> pdb=" O VAL A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.385A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A1844 " --> pdb=" O LYS A1840 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A1845 " --> pdb=" O HIS A1841 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A1846 " --> pdb=" O ILE A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.965A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.330A 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: 3.971A pdb=" N GLN A1905 " --> pdb=" O PRO A1901 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A1906 " --> pdb=" O VAL A1902 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A1917 " --> pdb=" O LEU A1913 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A1920 " --> pdb=" O CYS A1916 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A1925 " --> pdb=" O ARG A1921 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1927 " --> pdb=" O GLU A1923 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A1928 " --> pdb=" O ALA A1924 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1947 " --> pdb=" O ARG A1943 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A1950 " --> pdb=" O GLU A1946 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1968 removed outlier: 3.943A pdb=" N LYS A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Proline residue: A1968 - end of helix Processing helix chain 'A' and resid 1969 through 1978 removed outlier: 4.384A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.725A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A1998 " --> pdb=" O ASP A1994 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 4.714A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A2073 " --> pdb=" O TRP A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.743A pdb=" N LEU A2087 " --> pdb=" O ALA A2083 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A2088 " --> pdb=" O MET A2084 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2106 removed outlier: 3.881A pdb=" N ARG A2100 " --> pdb=" O GLY A2096 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A2102 " --> pdb=" O LEU A2098 " (cutoff:3.500A) Proline residue: A2103 - end of helix removed outlier: 5.565A pdb=" N TYR A2106 " --> pdb=" O LEU A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.755A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A2129 " --> pdb=" O GLN A2125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 removed outlier: 3.953A pdb=" N LYS A2140 " --> pdb=" O LYS A2136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A2141 " --> pdb=" O GLU A2137 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A2152 " --> pdb=" O ASP A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 removed outlier: 3.792A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.165A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.908A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A2195 " --> pdb=" O LYS A2191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A2200 " --> pdb=" O CYS A2196 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A2204 " --> pdb=" O LEU A2200 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.532A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 removed outlier: 3.652A pdb=" N SER A2225 " --> pdb=" O LEU A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2248 removed outlier: 4.233A pdb=" N VAL A2247 " --> pdb=" O ALA A2243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A2248 " --> pdb=" O ALA A2244 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2257 removed outlier: 4.013A pdb=" N LEU A2257 " --> pdb=" O LEU A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.652A pdb=" N LYS A2264 " --> pdb=" O PRO A2260 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A2266 " --> pdb=" O LEU A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2292 through 2307 removed outlier: 3.793A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A2299 " --> pdb=" O GLY A2295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A2301 " --> pdb=" O ARG A2297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A2302 " --> pdb=" O TYR A2298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A2307 " --> pdb=" O ARG A2303 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.631A pdb=" N ASN A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A2322 " --> pdb=" O ASN A2318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A2327 " --> pdb=" O LEU A2323 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 removed outlier: 3.823A pdb=" N ALA A2346 " --> pdb=" O GLY A2342 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A2349 " --> pdb=" O ALA A2345 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A2350 " --> pdb=" O ALA A2346 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A2351 " --> pdb=" O MET A2347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A2355 " --> pdb=" O ILE A2351 " (cutoff:3.500A) Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2412 removed outlier: 3.501A pdb=" N ILE A2388 " --> pdb=" O MET A2384 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A2389 " --> pdb=" O GLY A2385 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A2390 " --> pdb=" O ASN A2386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A2391 " --> pdb=" O ALA A2387 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A2396 " --> pdb=" O TYR A2392 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A2397 " --> pdb=" O SER A2393 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A2403 " --> pdb=" O LEU A2399 " (cutoff:3.500A) Proline residue: A2404 - end of helix removed outlier: 8.869A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 removed outlier: 3.722A pdb=" N ILE A2427 " --> pdb=" O LEU A2423 " (cutoff:3.500A) Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 removed outlier: 4.195A pdb=" N VAL A2435 " --> pdb=" O ASP A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.842A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A2466 " --> pdb=" O PRO A2462 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A2469 " --> pdb=" O LYS A2465 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 4.886A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 3.867A pdb=" N ALA A2498 " --> pdb=" O PRO A2494 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A2499 " --> pdb=" O ASP A2495 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A2500 " --> pdb=" O LEU A2496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A2501 " --> pdb=" O ARG A2497 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A2502 " --> pdb=" O ALA A2498 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.752A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 3.785A pdb=" N ARG A2518 " --> pdb=" O LEU A2514 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A2524 " --> pdb=" O LEU A2520 " (cutoff:3.500A) removed outlier: 5.609A 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: 4.694A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A2547 " --> pdb=" O SER A2543 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A2549 " --> pdb=" O ILE A2545 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS A2550 " --> pdb=" O ASP A2546 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A2555 " --> pdb=" O THR A2551 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A2557 " --> pdb=" O TYR A2553 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 4.153A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A2580 " --> pdb=" O ILE A2576 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 3.856A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A2589 " --> pdb=" O MET A2585 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.869A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.150A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2707 through 2712 removed outlier: 5.461A pdb=" N ILE A2711 " --> pdb=" O ASP A2707 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR A2712 " --> pdb=" O THR A2708 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2707 through 2712' Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.514A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.506A pdb=" N LEU A2763 " --> pdb=" O PRO A2759 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2759 through 2764' Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.540A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 3.517A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) Processing helix chain 'A' and resid 2835 through 2861 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.760A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 3.984A pdb=" N ALA A2883 " --> pdb=" O ALA A2879 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A2886 " --> pdb=" O LYS A2882 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A2897 " --> pdb=" O LEU A2893 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A2898 " --> pdb=" O LYS A2894 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2945 removed outlier: 3.542A pdb=" N SER A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 5.252A 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: 4.435A 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 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.567A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.344A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3150 removed outlier: 4.312A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3151 through 3166 removed outlier: 3.574A pdb=" N GLU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 4.315A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3175 through 3180' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.278A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.801A 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: 3.967A 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 3253 removed outlier: 4.315A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 5.555A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3293 through 3307 removed outlier: 3.883A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix Processing helix chain 'A' and resid 3311 through 3316 removed outlier: 4.321A pdb=" N LYS A3316 " --> pdb=" O PRO A3312 " (cutoff:3.500A) Processing helix chain 'A' and resid 3317 through 3330 Proline residue: A3321 - end of helix removed outlier: 4.216A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3605 Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.535A 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: 3.726A pdb=" N LEU A3619 " --> pdb=" O ARG A3615 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A3622 " --> pdb=" O ASN A3618 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A3625 " --> pdb=" O LEU A3621 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A3626 " --> pdb=" O GLN A3622 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 removed outlier: 3.553A pdb=" N GLU A3642 " --> pdb=" O ASP A3638 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.959A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 3.505A pdb=" N ALA A3675 " --> pdb=" O PHE A3671 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A3694 " --> pdb=" O ALA A3690 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A3695 " --> pdb=" O TYR A3691 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A3696 " --> pdb=" O ALA A3692 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A3697 " --> pdb=" O ASP A3693 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A3699 " --> pdb=" O MET A3695 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A3701 " --> pdb=" O LYS A3697 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.554A pdb=" N LEU A3724 " --> pdb=" O GLU A3720 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.646A pdb=" N VAL A3740 " --> pdb=" O ALA A3736 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 removed outlier: 3.509A pdb=" N ALA A3757 " --> pdb=" O PRO A3753 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A3760 " --> pdb=" O ALA A3756 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A3761 " --> pdb=" O ALA A3757 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A3763 " --> pdb=" O LEU A3759 " (cutoff:3.500A) Processing helix chain 'A' and resid 3770 through 3785 removed outlier: 3.511A pdb=" N LEU A3781 " --> pdb=" O MET A3777 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.609A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A3800 " --> pdb=" O LEU A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.764A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 4.001A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A3843 " --> pdb=" O LEU A3839 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.697A pdb=" N ASN A3856 " --> pdb=" O SER A3852 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A3857 " --> pdb=" O ASP A3853 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 3.774A pdb=" N VAL A3875 " --> pdb=" O ILE A3871 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A3877 " --> pdb=" O SER A3873 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A3887 " --> pdb=" O GLU A3883 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 removed outlier: 3.676A pdb=" N ASN A3905 " --> pdb=" O GLN A3901 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A3906 " --> pdb=" O GLY A3902 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A3912 " --> pdb=" O LYS A3908 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A3924 " --> pdb=" O LEU A3920 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 3.792A pdb=" N ALA A3936 " --> pdb=" O GLN A3932 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS A3937 " --> pdb=" O GLN A3933 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A3938 " --> pdb=" O SER A3934 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 3.566A pdb=" N GLY A3946 " --> pdb=" O ASP A3942 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A3949 " --> pdb=" O VAL A3945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A3953 " --> pdb=" O HIS A3949 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A3955 " --> pdb=" O PHE A3951 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.920A pdb=" N LEU A3968 " --> pdb=" O GLN A3964 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A3976 " --> pdb=" O MET A3972 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A3986 " --> pdb=" O LEU A3982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A3987 " --> pdb=" O LEU A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.567A pdb=" N PHE A4016 " --> pdb=" O MET A4012 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 removed outlier: 3.964A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.565A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.348A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 3.781A pdb=" N VAL A4084 " --> pdb=" O TYR A4080 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A4085 " --> pdb=" O GLU A4081 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A4087 " --> pdb=" O PHE A4083 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A4088 " --> pdb=" O VAL A4084 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.128A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 4.200A pdb=" N GLU A4120 " --> pdb=" O GLN A4116 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU A4121 " --> pdb=" O THR A4117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A4122 " --> pdb=" O PHE A4118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A4123 " --> pdb=" O LEU A4119 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4131 removed outlier: 3.718A pdb=" N GLN A4130 " --> pdb=" O LEU A4126 " (cutoff:3.500A) Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4162 removed outlier: 3.508A pdb=" N LYS A4162 " --> pdb=" O THR A4158 " (cutoff:3.500A) Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4181 through 4208 removed outlier: 3.847A pdb=" N LYS A4185 " --> pdb=" O GLY A4181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4258 removed outlier: 4.297A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4273 removed outlier: 4.392A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.770A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS A4310 " --> pdb=" O PHE A4306 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.966A pdb=" N ILE A4485 " --> pdb=" O TRP A4481 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 3.885A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A4510 " --> pdb=" O ALA A4506 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A4518 " --> pdb=" O ASN A4514 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.963A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 removed outlier: 3.522A pdb=" N SER A4667 " --> pdb=" O ARG A4663 " (cutoff:3.500A) Processing helix chain 'A' and resid 4675 through 4683 Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.880A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.793A pdb=" N TYR A4721 " --> pdb=" O ASN A4717 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4750 removed outlier: 4.992A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 4.413A pdb=" N THR A4755 " --> pdb=" O LYS A4751 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 removed outlier: 3.894A pdb=" N VAL A4768 " --> pdb=" O GLY A4764 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A4771 " --> pdb=" O LEU A4767 " (cutoff:3.500A) Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.351A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 5.236A 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: 3.727A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.765A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A4831 " --> pdb=" O ILE A4827 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4826 through 4832' Processing helix chain 'A' and resid 4839 through 4854 removed outlier: 3.793A pdb=" N ARG A4843 " --> pdb=" O TYR A4839 " (cutoff:3.500A) Processing helix chain 'A' and resid 4858 through 4887 removed outlier: 3.801A pdb=" N ILE A4862 " --> pdb=" O LEU A4858 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A4863 " --> pdb=" O LEU A4859 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A4871 " --> pdb=" O ILE A4867 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.894A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR A4900 " --> pdb=" O ASP A4896 " (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 removed outlier: 3.543A pdb=" N GLU A4963 " --> pdb=" O ARG A4959 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.027A pdb=" N ALA A 861 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.726A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A1776 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1772 through 1778' Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.863A pdb=" N ALA A 328 " --> pdb=" O ASP A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 4.601A pdb=" N ILE A2382 " --> pdb=" O GLU A2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.931A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 219 through 224 removed outlier: 5.719A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.683A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.736A pdb=" N HIS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 271' Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.611A pdb=" N ARG D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.972A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 removed outlier: 4.364A pdb=" N VAL D 452 " --> pdb=" O PRO D 448 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 461 " --> pdb=" O GLN D 457 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 493 removed outlier: 3.528A pdb=" N GLU D 491 " --> pdb=" O ASN D 487 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.608A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.634A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 3.727A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 529 " --> pdb=" O SER D 525 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.546A pdb=" N PHE D 551 " --> pdb=" O ASN D 547 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 555 " --> pdb=" O PHE D 551 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.137A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.587A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 590 removed outlier: 4.243A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 590' Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.536A pdb=" N SER D 596 " --> pdb=" O GLY D 592 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.831A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 613 " --> pdb=" O LYS D 609 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 removed outlier: 3.576A pdb=" N ILE D 632 " --> pdb=" O ASN D 628 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP D 634 " --> pdb=" O HIS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.592A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.767A 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 875 through 901 removed outlier: 4.035A pdb=" N ILE D 881 " --> pdb=" O HIS D 877 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 925 removed outlier: 3.944A pdb=" N LEU D 924 " --> pdb=" O GLU D 920 " (cutoff:3.500A) Proline residue: D 925 - end of helix No H-bonds generated for 'chain 'D' and resid 920 through 925' Processing helix chain 'D' and resid 926 through 947 Processing helix chain 'D' and resid 954 through 960 Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.968A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.788A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.359A 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: 7.153A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.878A 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 removed outlier: 4.182A pdb=" N MET D1421 " --> pdb=" O TYR D1417 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.421A 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: 3.832A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.308A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.823A 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: 3.765A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D1666 " --> pdb=" O SER D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.645A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS D1677 " --> pdb=" O ALA D1673 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 removed outlier: 3.612A pdb=" N ALA D1688 " --> pdb=" O GLN D1684 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE D1689 " --> pdb=" O LEU D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1710 removed outlier: 3.541A pdb=" N TYR D1703 " --> pdb=" O ARG D1699 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP D1704 " --> pdb=" O ALA D1700 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D1706 " --> pdb=" O TYR D1702 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D1707 " --> pdb=" O TYR D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.158A pdb=" N ALA D1715 " --> pdb=" O LEU D1711 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D1716 " --> pdb=" O SER D1712 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D1717 " --> pdb=" O SER D1713 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D1719 " --> pdb=" O ALA D1715 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 4.292A pdb=" N SER D1735 " --> pdb=" O GLU D1731 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 removed outlier: 3.625A pdb=" N LEU D1787 " --> pdb=" O PRO D1783 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D1788 " --> pdb=" O LEU D1784 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D1789 " --> pdb=" O ASP D1785 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 removed outlier: 3.691A pdb=" N VAL D1819 " --> pdb=" O GLU D1815 " (cutoff:3.500A) Proline residue: D1820 - end of helix removed outlier: 3.789A pdb=" N LYS D1823 " --> pdb=" O VAL D1819 " (cutoff:3.500A) Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.386A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D1844 " --> pdb=" O LYS D1840 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D1845 " --> pdb=" O HIS D1841 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D1846 " --> pdb=" O ILE D1842 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.965A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.329A 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: 3.972A pdb=" N GLN D1905 " --> pdb=" O PRO D1901 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D1906 " --> pdb=" O VAL D1902 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D1917 " --> pdb=" O LEU D1913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS D1920 " --> pdb=" O CYS D1916 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE D1925 " --> pdb=" O ARG D1921 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D1927 " --> pdb=" O GLU D1923 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D1928 " --> pdb=" O ALA D1924 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D1947 " --> pdb=" O ARG D1943 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D1950 " --> pdb=" O GLU D1946 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1968 removed outlier: 3.943A pdb=" N LYS D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Proline residue: D1968 - end of helix Processing helix chain 'D' and resid 1969 through 1978 removed outlier: 4.384A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.725A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D1998 " --> pdb=" O ASP D1994 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 4.714A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D2073 " --> pdb=" O TRP D2069 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.743A pdb=" N LEU D2087 " --> pdb=" O ALA D2083 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D2088 " --> pdb=" O MET D2084 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2106 removed outlier: 3.880A pdb=" N ARG D2100 " --> pdb=" O GLY D2096 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D2102 " --> pdb=" O LEU D2098 " (cutoff:3.500A) Proline residue: D2103 - end of helix removed outlier: 5.566A pdb=" N TYR D2106 " --> pdb=" O LEU D2102 " (cutoff:3.500A) Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.754A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D2129 " --> pdb=" O GLN D2125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 removed outlier: 3.954A pdb=" N LYS D2140 " --> pdb=" O LYS D2136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D2141 " --> pdb=" O GLU D2137 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D2152 " --> pdb=" O ASP D2148 " (cutoff:3.500A) Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 removed outlier: 3.791A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.164A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.908A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D2195 " --> pdb=" O LYS D2191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D2200 " --> pdb=" O CYS D2196 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D2204 " --> pdb=" O LEU D2200 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.531A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 removed outlier: 3.652A pdb=" N SER D2225 " --> pdb=" O LEU D2221 " (cutoff:3.500A) Processing helix chain 'D' and resid 2238 through 2248 removed outlier: 4.233A pdb=" N VAL D2247 " --> pdb=" O ALA D2243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D2248 " --> pdb=" O ALA D2244 " (cutoff:3.500A) Processing helix chain 'D' and resid 2250 through 2257 removed outlier: 4.012A pdb=" N LEU D2257 " --> pdb=" O LEU D2253 " (cutoff:3.500A) Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.653A pdb=" N LYS D2264 " --> pdb=" O PRO D2260 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D2266 " --> pdb=" O LEU D2262 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2292 through 2307 removed outlier: 3.793A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D2299 " --> pdb=" O GLY D2295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE D2301 " --> pdb=" O ARG D2297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D2302 " --> pdb=" O TYR D2298 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D2307 " --> pdb=" O ARG D2303 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.632A pdb=" N ASN D2318 " --> pdb=" O GLU D2314 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG D2322 " --> pdb=" O ASN D2318 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D2326 " --> pdb=" O ARG D2322 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D2327 " --> pdb=" O LEU D2323 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 removed outlier: 3.823A pdb=" N ALA D2346 " --> pdb=" O GLY D2342 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D2349 " --> pdb=" O ALA D2345 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D2350 " --> pdb=" O ALA D2346 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE D2351 " --> pdb=" O MET D2347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU D2355 " --> pdb=" O ILE D2351 " (cutoff:3.500A) Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2412 removed outlier: 4.135A pdb=" N MET D2389 " --> pdb=" O GLY D2385 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR D2390 " --> pdb=" O ASN D2386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D2391 " --> pdb=" O ALA D2387 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D2396 " --> pdb=" O TYR D2392 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D2397 " --> pdb=" O SER D2393 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D2403 " --> pdb=" O LEU D2399 " (cutoff:3.500A) Proline residue: D2404 - end of helix removed outlier: 8.870A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D2409 " --> pdb=" O GLU D2405 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 removed outlier: 3.722A pdb=" N ILE D2427 " --> pdb=" O LEU D2423 " (cutoff:3.500A) Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 removed outlier: 4.194A pdb=" N VAL D2435 " --> pdb=" O ASP D2431 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.841A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D2466 " --> pdb=" O PRO D2462 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D2469 " --> pdb=" O LYS D2465 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 4.885A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 3.866A pdb=" N ALA D2498 " --> pdb=" O PRO D2494 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D2499 " --> pdb=" O ASP D2495 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA D2500 " --> pdb=" O LEU D2496 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D2501 " --> pdb=" O ARG D2497 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D2502 " --> pdb=" O ALA D2498 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.753A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 3.784A pdb=" N ARG D2518 " --> pdb=" O LEU D2514 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D2524 " --> pdb=" O LEU D2520 " (cutoff:3.500A) removed outlier: 5.609A 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: 4.693A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D2547 " --> pdb=" O SER D2543 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU D2549 " --> pdb=" O ILE D2545 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS D2550 " --> pdb=" O ASP D2546 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D2555 " --> pdb=" O THR D2551 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D2557 " --> pdb=" O TYR D2553 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 4.153A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D2580 " --> pdb=" O ILE D2576 " (cutoff:3.500A) Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 3.855A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU D2589 " --> pdb=" O MET D2585 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.870A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.149A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2658 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2707 through 2712 removed outlier: 5.461A pdb=" N ILE D2711 " --> pdb=" O ASP D2707 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR D2712 " --> pdb=" O THR D2708 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2707 through 2712' Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.514A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 3.506A pdb=" N LEU D2763 " --> pdb=" O PRO D2759 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2759 through 2764' Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.541A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 3.516A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) Processing helix chain 'D' and resid 2835 through 2861 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.760A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 3.984A pdb=" N ALA D2883 " --> pdb=" O ALA D2879 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG D2886 " --> pdb=" O LYS D2882 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN D2897 " --> pdb=" O LEU D2893 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D2898 " --> pdb=" O LYS D2894 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2945 removed outlier: 3.543A pdb=" N SER D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 5.253A 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: 4.434A 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 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.567A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.344A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3150 removed outlier: 4.313A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3151 through 3166 removed outlier: 3.574A pdb=" N GLU D3157 " --> pdb=" O SER D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 4.315A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3175 through 3180' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.278A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.801A 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: 3.967A 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 3253 removed outlier: 4.316A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 5.555A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Processing helix chain 'D' and resid 3269 through 3288 Processing helix chain 'D' and resid 3293 through 3307 removed outlier: 3.882A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix Processing helix chain 'D' and resid 3311 through 3316 removed outlier: 4.322A pdb=" N LYS D3316 " --> pdb=" O PRO D3312 " (cutoff:3.500A) Processing helix chain 'D' and resid 3317 through 3330 Proline residue: D3321 - end of helix removed outlier: 4.216A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3605 Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.535A 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: 3.727A pdb=" N LEU D3619 " --> pdb=" O ARG D3615 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D3622 " --> pdb=" O ASN D3618 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D3625 " --> pdb=" O LEU D3621 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D3626 " --> pdb=" O GLN D3622 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 removed outlier: 3.554A pdb=" N GLU D3642 " --> pdb=" O ASP D3638 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.960A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 3.505A pdb=" N ALA D3675 " --> pdb=" O PHE D3671 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D3694 " --> pdb=" O ALA D3690 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET D3695 " --> pdb=" O TYR D3691 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D3696 " --> pdb=" O ALA D3692 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D3697 " --> pdb=" O ASP D3693 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS D3699 " --> pdb=" O MET D3695 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP D3701 " --> pdb=" O LYS D3697 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.553A pdb=" N LEU D3724 " --> pdb=" O GLU D3720 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.646A pdb=" N VAL D3740 " --> pdb=" O ALA D3736 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 removed outlier: 3.509A pdb=" N ALA D3757 " --> pdb=" O PRO D3753 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D3760 " --> pdb=" O ALA D3756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D3761 " --> pdb=" O ALA D3757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D3763 " --> pdb=" O LEU D3759 " (cutoff:3.500A) Processing helix chain 'D' and resid 3770 through 3785 removed outlier: 3.511A pdb=" N LEU D3781 " --> pdb=" O MET D3777 " (cutoff:3.500A) Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.610A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D3800 " --> pdb=" O LEU D3796 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.764A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 4.002A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D3843 " --> pdb=" O LEU D3839 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.699A pdb=" N ASN D3856 " --> pdb=" O SER D3852 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D3857 " --> pdb=" O ASP D3853 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 3.774A pdb=" N VAL D3875 " --> pdb=" O ILE D3871 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D3877 " --> pdb=" O SER D3873 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP D3887 " --> pdb=" O GLU D3883 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 removed outlier: 3.677A pdb=" N ASN D3905 " --> pdb=" O GLN D3901 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D3906 " --> pdb=" O GLY D3902 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D3912 " --> pdb=" O LYS D3908 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D3924 " --> pdb=" O LEU D3920 " (cutoff:3.500A) Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 3.792A pdb=" N ALA D3936 " --> pdb=" O GLN D3932 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS D3937 " --> pdb=" O GLN D3933 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D3938 " --> pdb=" O SER D3934 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 3.566A pdb=" N GLY D3946 " --> pdb=" O ASP D3942 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS D3949 " --> pdb=" O VAL D3945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS D3953 " --> pdb=" O HIS D3949 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN D3955 " --> pdb=" O PHE D3951 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.920A pdb=" N LEU D3968 " --> pdb=" O GLN D3964 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS D3976 " --> pdb=" O MET D3972 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D3986 " --> pdb=" O LEU D3982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D3987 " --> pdb=" O LEU D3983 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.567A pdb=" N PHE D4016 " --> pdb=" O MET D4012 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 removed outlier: 3.964A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.564A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.348A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 3.781A pdb=" N VAL D4084 " --> pdb=" O TYR D4080 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D4085 " --> pdb=" O GLU D4081 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D4087 " --> pdb=" O PHE D4083 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS D4088 " --> pdb=" O VAL D4084 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.128A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 4.199A pdb=" N GLU D4120 " --> pdb=" O GLN D4116 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D4121 " --> pdb=" O THR D4117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D4122 " --> pdb=" O PHE D4118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D4123 " --> pdb=" O LEU D4119 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4131 removed outlier: 3.719A pdb=" N GLN D4130 " --> pdb=" O LEU D4126 " (cutoff:3.500A) Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4162 removed outlier: 3.508A pdb=" N LYS D4162 " --> pdb=" O THR D4158 " (cutoff:3.500A) Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4181 through 4208 removed outlier: 3.847A pdb=" N LYS D4185 " --> pdb=" O GLY D4181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4258 removed outlier: 4.297A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4273 removed outlier: 4.392A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.769A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS D4310 " --> pdb=" O PHE D4306 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.966A pdb=" N ILE D4485 " --> pdb=" O TRP D4481 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 3.885A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D4510 " --> pdb=" O ALA D4506 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D4518 " --> pdb=" O ASN D4514 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.962A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 removed outlier: 3.522A pdb=" N SER D4667 " --> pdb=" O ARG D4663 " (cutoff:3.500A) Processing helix chain 'D' and resid 4675 through 4683 Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.881A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.793A pdb=" N TYR D4721 " --> pdb=" O ASN D4717 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4750 removed outlier: 4.993A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4751 through 4762 removed outlier: 4.413A pdb=" N THR D4755 " --> pdb=" O LYS D4751 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 removed outlier: 3.894A pdb=" N VAL D4768 " --> pdb=" O GLY D4764 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D4771 " --> pdb=" O LEU D4767 " (cutoff:3.500A) Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.353A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 5.236A 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: 3.727A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.766A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D4831 " --> pdb=" O ILE D4827 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4826 through 4832' Processing helix chain 'D' and resid 4839 through 4854 removed outlier: 3.793A pdb=" N ARG D4843 " --> pdb=" O TYR D4839 " (cutoff:3.500A) Processing helix chain 'D' and resid 4858 through 4887 removed outlier: 3.800A pdb=" N ILE D4862 " --> pdb=" O LEU D4858 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D4863 " --> pdb=" O LEU D4859 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D4871 " --> pdb=" O ILE D4867 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.894A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR D4900 " --> pdb=" O ASP D4896 " (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 removed outlier: 3.543A pdb=" N GLU D4963 " --> pdb=" O ARG D4959 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.027A pdb=" N ALA D 861 " --> pdb=" O THR D 858 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.725A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR D1776 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1772 through 1778' Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.862A pdb=" N ALA D 328 " --> pdb=" O ASP D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 323 through 328' Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 4.602A pdb=" N ILE D2382 " --> pdb=" O GLU D2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.931A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 219 through 224 removed outlier: 5.719A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.683A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.737A pdb=" N HIS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.611A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.972A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 4.365A pdb=" N VAL B 452 " --> pdb=" O PRO B 448 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 removed outlier: 3.529A pdb=" N GLU B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.608A pdb=" N VAL B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.634A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 3.727A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.545A pdb=" N PHE B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.137A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.587A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 4.243A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 590' Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.535A pdb=" N SER B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.832A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 removed outlier: 3.575A pdb=" N ILE B 632 " --> pdb=" O ASN B 628 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.592A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.766A 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 875 through 901 removed outlier: 4.035A pdb=" N ILE B 881 " --> pdb=" O HIS B 877 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.944A pdb=" N LEU B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Proline residue: B 925 - end of helix No H-bonds generated for 'chain 'B' and resid 920 through 925' Processing helix chain 'B' and resid 926 through 947 Processing helix chain 'B' and resid 954 through 960 Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.966A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.789A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.358A 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: 7.152A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.879A 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 removed outlier: 4.180A pdb=" N MET B1421 " --> pdb=" O TYR B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.420A 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: 3.833A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.308A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.823A 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: 3.765A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B1666 " --> pdb=" O SER B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.646A pdb=" N ALA B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B1677 " --> pdb=" O ALA B1673 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 removed outlier: 3.612A pdb=" N ALA B1688 " --> pdb=" O GLN B1684 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B1689 " --> pdb=" O LEU B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1710 removed outlier: 3.541A pdb=" N TYR B1703 " --> pdb=" O ARG B1699 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B1704 " --> pdb=" O ALA B1700 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B1706 " --> pdb=" O TYR B1702 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B1707 " --> pdb=" O TYR B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.157A pdb=" N ALA B1715 " --> pdb=" O LEU B1711 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B1716 " --> pdb=" O SER B1712 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B1717 " --> pdb=" O SER B1713 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B1719 " --> pdb=" O ALA B1715 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 4.293A pdb=" N SER B1735 " --> pdb=" O GLU B1731 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 removed outlier: 3.626A pdb=" N LEU B1787 " --> pdb=" O PRO B1783 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B1788 " --> pdb=" O LEU B1784 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B1789 " --> pdb=" O ASP B1785 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 removed outlier: 3.692A pdb=" N VAL B1819 " --> pdb=" O GLU B1815 " (cutoff:3.500A) Proline residue: B1820 - end of helix removed outlier: 3.789A pdb=" N LYS B1823 " --> pdb=" O VAL B1819 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.386A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B1844 " --> pdb=" O LYS B1840 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B1845 " --> pdb=" O HIS B1841 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B1846 " --> pdb=" O ILE B1842 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.966A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.329A 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: 3.972A pdb=" N GLN B1905 " --> pdb=" O PRO B1901 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B1906 " --> pdb=" O VAL B1902 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B1917 " --> pdb=" O LEU B1913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B1920 " --> pdb=" O CYS B1916 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B1925 " --> pdb=" O ARG B1921 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B1927 " --> pdb=" O GLU B1923 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B1928 " --> pdb=" O ALA B1924 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B1947 " --> pdb=" O ARG B1943 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B1950 " --> pdb=" O GLU B1946 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1968 removed outlier: 3.943A pdb=" N LYS B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Proline residue: B1968 - end of helix Processing helix chain 'B' and resid 1969 through 1978 removed outlier: 4.384A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.725A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B1998 " --> pdb=" O ASP B1994 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 4.714A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B2073 " --> pdb=" O TRP B2069 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.742A pdb=" N LEU B2087 " --> pdb=" O ALA B2083 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B2088 " --> pdb=" O MET B2084 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2106 removed outlier: 3.880A pdb=" N ARG B2100 " --> pdb=" O GLY B2096 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B2102 " --> pdb=" O LEU B2098 " (cutoff:3.500A) Proline residue: B2103 - end of helix removed outlier: 5.566A pdb=" N TYR B2106 " --> pdb=" O LEU B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.754A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B2129 " --> pdb=" O GLN B2125 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 removed outlier: 3.953A pdb=" N LYS B2140 " --> pdb=" O LYS B2136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B2141 " --> pdb=" O GLU B2137 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B2152 " --> pdb=" O ASP B2148 " (cutoff:3.500A) Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 removed outlier: 3.792A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.165A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.907A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B2195 " --> pdb=" O LYS B2191 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B2200 " --> pdb=" O CYS B2196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B2204 " --> pdb=" O LEU B2200 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.532A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 removed outlier: 3.651A pdb=" N SER B2225 " --> pdb=" O LEU B2221 " (cutoff:3.500A) Processing helix chain 'B' and resid 2238 through 2248 removed outlier: 4.232A pdb=" N VAL B2247 " --> pdb=" O ALA B2243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B2248 " --> pdb=" O ALA B2244 " (cutoff:3.500A) Processing helix chain 'B' and resid 2250 through 2257 removed outlier: 4.013A pdb=" N LEU B2257 " --> pdb=" O LEU B2253 " (cutoff:3.500A) Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.652A pdb=" N LYS B2264 " --> pdb=" O PRO B2260 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B2266 " --> pdb=" O LEU B2262 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2292 through 2307 removed outlier: 3.792A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B2299 " --> pdb=" O GLY B2295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B2301 " --> pdb=" O ARG B2297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B2302 " --> pdb=" O TYR B2298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B2307 " --> pdb=" O ARG B2303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.632A pdb=" N ASN B2318 " --> pdb=" O GLU B2314 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B2322 " --> pdb=" O ASN B2318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B2327 " --> pdb=" O LEU B2323 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 removed outlier: 3.823A pdb=" N ALA B2346 " --> pdb=" O GLY B2342 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B2349 " --> pdb=" O ALA B2345 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B2350 " --> pdb=" O ALA B2346 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B2351 " --> pdb=" O MET B2347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU B2355 " --> pdb=" O ILE B2351 " (cutoff:3.500A) Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2412 removed outlier: 3.500A pdb=" N ILE B2388 " --> pdb=" O MET B2384 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B2389 " --> pdb=" O GLY B2385 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B2390 " --> pdb=" O ASN B2386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B2391 " --> pdb=" O ALA B2387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B2396 " --> pdb=" O TYR B2392 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B2397 " --> pdb=" O SER B2393 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B2403 " --> pdb=" O LEU B2399 " (cutoff:3.500A) Proline residue: B2404 - end of helix removed outlier: 8.870A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B2409 " --> pdb=" O GLU B2405 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 removed outlier: 3.723A pdb=" N ILE B2427 " --> pdb=" O LEU B2423 " (cutoff:3.500A) Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 removed outlier: 4.194A pdb=" N VAL B2435 " --> pdb=" O ASP B2431 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.841A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B2466 " --> pdb=" O PRO B2462 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B2469 " --> pdb=" O LYS B2465 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 4.886A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 3.867A pdb=" N ALA B2498 " --> pdb=" O PRO B2494 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B2499 " --> pdb=" O ASP B2495 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B2500 " --> pdb=" O LEU B2496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B2501 " --> pdb=" O ARG B2497 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B2502 " --> pdb=" O ALA B2498 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.753A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 3.784A pdb=" N ARG B2518 " --> pdb=" O LEU B2514 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B2524 " --> pdb=" O LEU B2520 " (cutoff:3.500A) removed outlier: 5.609A 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: 4.694A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B2547 " --> pdb=" O SER B2543 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B2549 " --> pdb=" O ILE B2545 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS B2550 " --> pdb=" O ASP B2546 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B2555 " --> pdb=" O THR B2551 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B2557 " --> pdb=" O TYR B2553 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 4.153A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B2580 " --> pdb=" O ILE B2576 " (cutoff:3.500A) Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 3.856A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B2589 " --> pdb=" O MET B2585 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.869A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.150A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2658 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2707 through 2712 removed outlier: 5.460A pdb=" N ILE B2711 " --> pdb=" O ASP B2707 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR B2712 " --> pdb=" O THR B2708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2707 through 2712' Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.513A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 3.506A pdb=" N LEU B2763 " --> pdb=" O PRO B2759 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2759 through 2764' Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.541A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 3.516A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) Processing helix chain 'B' and resid 2835 through 2861 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.760A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 3.984A pdb=" N ALA B2883 " --> pdb=" O ALA B2879 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG B2886 " --> pdb=" O LYS B2882 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN B2897 " --> pdb=" O LEU B2893 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B2898 " --> pdb=" O LYS B2894 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2945 removed outlier: 3.542A pdb=" N SER B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 5.252A 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: 4.435A 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 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.567A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.343A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3150 removed outlier: 4.313A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3151 through 3166 removed outlier: 3.574A pdb=" N GLU B3157 " --> pdb=" O SER B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 4.316A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3175 through 3180' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.278A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.801A 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: 3.967A 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 3253 removed outlier: 4.314A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 5.555A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3269 through 3288 Processing helix chain 'B' and resid 3293 through 3307 removed outlier: 3.884A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix Processing helix chain 'B' and resid 3311 through 3316 removed outlier: 4.322A pdb=" N LYS B3316 " --> pdb=" O PRO B3312 " (cutoff:3.500A) Processing helix chain 'B' and resid 3317 through 3330 Proline residue: B3321 - end of helix removed outlier: 4.216A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3605 Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.535A 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: 3.726A pdb=" N LEU B3619 " --> pdb=" O ARG B3615 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B3622 " --> pdb=" O ASN B3618 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B3625 " --> pdb=" O LEU B3621 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS B3626 " --> pdb=" O GLN B3622 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 removed outlier: 3.554A pdb=" N GLU B3642 " --> pdb=" O ASP B3638 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.959A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 3.506A pdb=" N ALA B3675 " --> pdb=" O PHE B3671 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B3694 " --> pdb=" O ALA B3690 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B3695 " --> pdb=" O TYR B3691 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B3696 " --> pdb=" O ALA B3692 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B3697 " --> pdb=" O ASP B3693 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B3699 " --> pdb=" O MET B3695 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B3701 " --> pdb=" O LYS B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.554A pdb=" N LEU B3724 " --> pdb=" O GLU B3720 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.646A pdb=" N VAL B3740 " --> pdb=" O ALA B3736 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 removed outlier: 3.509A pdb=" N ALA B3757 " --> pdb=" O PRO B3753 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B3760 " --> pdb=" O ALA B3756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B3761 " --> pdb=" O ALA B3757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B3763 " --> pdb=" O LEU B3759 " (cutoff:3.500A) Processing helix chain 'B' and resid 3770 through 3785 removed outlier: 3.511A pdb=" N LEU B3781 " --> pdb=" O MET B3777 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.609A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B3800 " --> pdb=" O LEU B3796 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.763A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 4.001A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B3843 " --> pdb=" O LEU B3839 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.698A pdb=" N ASN B3856 " --> pdb=" O SER B3852 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR B3857 " --> pdb=" O ASP B3853 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 3.775A pdb=" N VAL B3875 " --> pdb=" O ILE B3871 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B3877 " --> pdb=" O SER B3873 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B3887 " --> pdb=" O GLU B3883 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 removed outlier: 3.677A pdb=" N ASN B3905 " --> pdb=" O GLN B3901 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B3906 " --> pdb=" O GLY B3902 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B3912 " --> pdb=" O LYS B3908 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B3924 " --> pdb=" O LEU B3920 " (cutoff:3.500A) Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 3.791A pdb=" N ALA B3936 " --> pdb=" O GLN B3932 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS B3937 " --> pdb=" O GLN B3933 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B3938 " --> pdb=" O SER B3934 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 3.566A pdb=" N GLY B3946 " --> pdb=" O ASP B3942 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B3949 " --> pdb=" O VAL B3945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B3953 " --> pdb=" O HIS B3949 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B3955 " --> pdb=" O PHE B3951 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.921A pdb=" N LEU B3968 " --> pdb=" O GLN B3964 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B3976 " --> pdb=" O MET B3972 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B3986 " --> pdb=" O LEU B3982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B3987 " --> pdb=" O LEU B3983 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.567A pdb=" N PHE B4016 " --> pdb=" O MET B4012 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 removed outlier: 3.964A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.565A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.348A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 3.781A pdb=" N VAL B4084 " --> pdb=" O TYR B4080 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B4085 " --> pdb=" O GLU B4081 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B4087 " --> pdb=" O PHE B4083 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B4088 " --> pdb=" O VAL B4084 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.129A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 4.200A pdb=" N GLU B4120 " --> pdb=" O GLN B4116 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU B4121 " --> pdb=" O THR B4117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B4122 " --> pdb=" O PHE B4118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B4123 " --> pdb=" O LEU B4119 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4131 removed outlier: 3.719A pdb=" N GLN B4130 " --> pdb=" O LEU B4126 " (cutoff:3.500A) Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4162 removed outlier: 3.508A pdb=" N LYS B4162 " --> pdb=" O THR B4158 " (cutoff:3.500A) Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4181 through 4208 removed outlier: 3.847A pdb=" N LYS B4185 " --> pdb=" O GLY B4181 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4258 removed outlier: 4.297A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4273 removed outlier: 4.392A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.769A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS B4310 " --> pdb=" O PHE B4306 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.966A pdb=" N ILE B4485 " --> pdb=" O TRP B4481 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 3.884A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B4510 " --> pdb=" O ALA B4506 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B4518 " --> pdb=" O ASN B4514 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.139A 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: 3.963A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 removed outlier: 3.522A pdb=" N SER B4667 " --> pdb=" O ARG B4663 " (cutoff:3.500A) Processing helix chain 'B' and resid 4675 through 4683 Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.882A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.793A pdb=" N TYR B4721 " --> pdb=" O ASN B4717 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4750 removed outlier: 4.993A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4751 through 4762 removed outlier: 4.412A pdb=" N THR B4755 " --> pdb=" O LYS B4751 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 removed outlier: 3.893A pdb=" N VAL B4768 " --> pdb=" O GLY B4764 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B4771 " --> pdb=" O LEU B4767 " (cutoff:3.500A) Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.353A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 5.236A 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: 3.726A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.765A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B4831 " --> pdb=" O ILE B4827 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4826 through 4832' Processing helix chain 'B' and resid 4839 through 4854 removed outlier: 3.792A pdb=" N ARG B4843 " --> pdb=" O TYR B4839 " (cutoff:3.500A) Processing helix chain 'B' and resid 4858 through 4887 removed outlier: 3.801A pdb=" N ILE B4862 " --> pdb=" O LEU B4858 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B4863 " --> pdb=" O LEU B4859 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B4871 " --> pdb=" O ILE B4867 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.894A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B4900 " --> pdb=" O ASP B4896 " (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 removed outlier: 3.542A pdb=" N GLU B4963 " --> pdb=" O ARG B4959 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.027A pdb=" N ALA B 861 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.724A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR B1776 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1772 through 1778' Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.864A pdb=" N ALA B 328 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 328' Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 4.602A pdb=" N ILE B2382 " --> pdb=" O GLU B2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.931A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 219 through 224 removed outlier: 5.718A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.683A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.737A pdb=" N HIS C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.611A pdb=" N ARG C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.971A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 removed outlier: 4.365A pdb=" N VAL C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 461 " --> pdb=" O GLN C 457 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 493 removed outlier: 3.529A pdb=" N GLU C 491 " --> pdb=" O ASN C 487 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.607A pdb=" N VAL C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.634A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.728A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 529 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.545A pdb=" N PHE C 551 " --> pdb=" O ASN C 547 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.137A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.586A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 removed outlier: 4.243A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 590' Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.535A pdb=" N SER C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.832A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 613 " --> pdb=" O LYS C 609 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.574A pdb=" N ILE C 632 " --> pdb=" O ASN C 628 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP C 634 " --> pdb=" O HIS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.592A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.766A 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 875 through 901 removed outlier: 4.035A pdb=" N ILE C 881 " --> pdb=" O HIS C 877 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 removed outlier: 3.944A pdb=" N LEU C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Proline residue: C 925 - end of helix No H-bonds generated for 'chain 'C' and resid 920 through 925' Processing helix chain 'C' and resid 926 through 947 Processing helix chain 'C' and resid 954 through 960 Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.967A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.789A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.359A 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: 7.153A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.878A 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 removed outlier: 4.182A pdb=" N MET C1421 " --> pdb=" O TYR C1417 " (cutoff:3.500A) Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.793A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.420A 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: 3.833A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.309A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.823A 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: 3.766A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C1666 " --> pdb=" O SER C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.645A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C1677 " --> pdb=" O ALA C1673 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 removed outlier: 3.611A pdb=" N ALA C1688 " --> pdb=" O GLN C1684 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C1689 " --> pdb=" O LEU C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1710 removed outlier: 3.541A pdb=" N TYR C1703 " --> pdb=" O ARG C1699 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP C1704 " --> pdb=" O ALA C1700 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C1706 " --> pdb=" O TYR C1702 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C1707 " --> pdb=" O TYR C1703 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.157A pdb=" N ALA C1715 " --> pdb=" O LEU C1711 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1716 " --> pdb=" O SER C1712 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C1717 " --> pdb=" O SER C1713 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C1719 " --> pdb=" O ALA C1715 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 4.293A pdb=" N SER C1735 " --> pdb=" O GLU C1731 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 removed outlier: 3.625A pdb=" N LEU C1787 " --> pdb=" O PRO C1783 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C1788 " --> pdb=" O LEU C1784 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C1789 " --> pdb=" O ASP C1785 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 removed outlier: 3.692A pdb=" N VAL C1819 " --> pdb=" O GLU C1815 " (cutoff:3.500A) Proline residue: C1820 - end of helix removed outlier: 3.789A pdb=" N LYS C1823 " --> pdb=" O VAL C1819 " (cutoff:3.500A) Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.386A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C1844 " --> pdb=" O LYS C1840 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C1845 " --> pdb=" O HIS C1841 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C1846 " --> pdb=" O ILE C1842 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.966A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.328A 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: 3.972A pdb=" N GLN C1905 " --> pdb=" O PRO C1901 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C1906 " --> pdb=" O VAL C1902 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C1917 " --> pdb=" O LEU C1913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS C1920 " --> pdb=" O CYS C1916 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C1925 " --> pdb=" O ARG C1921 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1927 " --> pdb=" O GLU C1923 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C1928 " --> pdb=" O ALA C1924 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C1947 " --> pdb=" O ARG C1943 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C1950 " --> pdb=" O GLU C1946 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1968 removed outlier: 3.942A pdb=" N LYS C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Proline residue: C1968 - end of helix Processing helix chain 'C' and resid 1969 through 1978 removed outlier: 4.384A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.725A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C1998 " --> pdb=" O ASP C1994 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 4.714A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C2073 " --> pdb=" O TRP C2069 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.742A pdb=" N LEU C2087 " --> pdb=" O ALA C2083 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C2088 " --> pdb=" O MET C2084 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2106 removed outlier: 3.881A pdb=" N ARG C2100 " --> pdb=" O GLY C2096 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C2102 " --> pdb=" O LEU C2098 " (cutoff:3.500A) Proline residue: C2103 - end of helix removed outlier: 5.567A pdb=" N TYR C2106 " --> pdb=" O LEU C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.753A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C2129 " --> pdb=" O GLN C2125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 removed outlier: 3.954A pdb=" N LYS C2140 " --> pdb=" O LYS C2136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C2141 " --> pdb=" O GLU C2137 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C2152 " --> pdb=" O ASP C2148 " (cutoff:3.500A) Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 removed outlier: 3.792A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.165A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.908A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C2195 " --> pdb=" O LYS C2191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C2200 " --> pdb=" O CYS C2196 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C2204 " --> pdb=" O LEU C2200 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.532A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 removed outlier: 3.651A pdb=" N SER C2225 " --> pdb=" O LEU C2221 " (cutoff:3.500A) Processing helix chain 'C' and resid 2238 through 2248 removed outlier: 4.233A pdb=" N VAL C2247 " --> pdb=" O ALA C2243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C2248 " --> pdb=" O ALA C2244 " (cutoff:3.500A) Processing helix chain 'C' and resid 2250 through 2257 removed outlier: 4.013A pdb=" N LEU C2257 " --> pdb=" O LEU C2253 " (cutoff:3.500A) Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.653A pdb=" N LYS C2264 " --> pdb=" O PRO C2260 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C2266 " --> pdb=" O LEU C2262 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2292 through 2307 removed outlier: 3.793A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C2299 " --> pdb=" O GLY C2295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE C2301 " --> pdb=" O ARG C2297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C2302 " --> pdb=" O TYR C2298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C2307 " --> pdb=" O ARG C2303 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.631A pdb=" N ASN C2318 " --> pdb=" O GLU C2314 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C2322 " --> pdb=" O ASN C2318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C2326 " --> pdb=" O ARG C2322 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C2327 " --> pdb=" O LEU C2323 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 removed outlier: 3.822A pdb=" N ALA C2346 " --> pdb=" O GLY C2342 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C2349 " --> pdb=" O ALA C2345 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C2350 " --> pdb=" O ALA C2346 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE C2351 " --> pdb=" O MET C2347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU C2355 " --> pdb=" O ILE C2351 " (cutoff:3.500A) Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2412 removed outlier: 4.134A pdb=" N MET C2389 " --> pdb=" O GLY C2385 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C2390 " --> pdb=" O ASN C2386 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C2391 " --> pdb=" O ALA C2387 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C2396 " --> pdb=" O TYR C2392 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C2397 " --> pdb=" O SER C2393 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C2403 " --> pdb=" O LEU C2399 " (cutoff:3.500A) Proline residue: C2404 - end of helix removed outlier: 8.870A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE C2409 " --> pdb=" O GLU C2405 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 removed outlier: 3.722A pdb=" N ILE C2427 " --> pdb=" O LEU C2423 " (cutoff:3.500A) Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 removed outlier: 4.194A pdb=" N VAL C2435 " --> pdb=" O ASP C2431 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.841A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C2466 " --> pdb=" O PRO C2462 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C2469 " --> pdb=" O LYS C2465 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 4.886A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 3.866A pdb=" N ALA C2498 " --> pdb=" O PRO C2494 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C2499 " --> pdb=" O ASP C2495 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA C2500 " --> pdb=" O LEU C2496 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C2501 " --> pdb=" O ARG C2497 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C2502 " --> pdb=" O ALA C2498 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.753A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 3.785A pdb=" N ARG C2518 " --> pdb=" O LEU C2514 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C2524 " --> pdb=" O LEU C2520 " (cutoff:3.500A) removed outlier: 5.610A 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: 4.694A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C2547 " --> pdb=" O SER C2543 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C2549 " --> pdb=" O ILE C2545 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS C2550 " --> pdb=" O ASP C2546 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU C2555 " --> pdb=" O THR C2551 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C2557 " --> pdb=" O TYR C2553 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 4.153A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C2580 " --> pdb=" O ILE C2576 " (cutoff:3.500A) Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 3.855A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU C2589 " --> pdb=" O MET C2585 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.869A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.150A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2658 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2707 through 2712 removed outlier: 5.461A pdb=" N ILE C2711 " --> pdb=" O ASP C2707 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR C2712 " --> pdb=" O THR C2708 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2707 through 2712' Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.513A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 3.506A pdb=" N LEU C2763 " --> pdb=" O PRO C2759 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2759 through 2764' Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.541A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 3.516A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) Processing helix chain 'C' and resid 2835 through 2861 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.759A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 3.984A pdb=" N ALA C2883 " --> pdb=" O ALA C2879 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG C2886 " --> pdb=" O LYS C2882 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C2897 " --> pdb=" O LEU C2893 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C2898 " --> pdb=" O LYS C2894 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2945 removed outlier: 3.543A pdb=" N SER C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 5.252A 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: 4.435A 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 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.567A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.343A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3150 removed outlier: 4.312A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3151 through 3166 removed outlier: 3.574A pdb=" N GLU C3157 " --> pdb=" O SER C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 4.316A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3175 through 3180' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.278A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.801A 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: 3.967A 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 3253 removed outlier: 4.315A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 5.555A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Processing helix chain 'C' and resid 3269 through 3288 Processing helix chain 'C' and resid 3293 through 3307 removed outlier: 3.883A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix Processing helix chain 'C' and resid 3311 through 3316 removed outlier: 4.321A pdb=" N LYS C3316 " --> pdb=" O PRO C3312 " (cutoff:3.500A) Processing helix chain 'C' and resid 3317 through 3330 Proline residue: C3321 - end of helix removed outlier: 4.215A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3605 Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.534A 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: 3.727A pdb=" N LEU C3619 " --> pdb=" O ARG C3615 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C3622 " --> pdb=" O ASN C3618 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C3625 " --> pdb=" O LEU C3621 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C3626 " --> pdb=" O GLN C3622 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 removed outlier: 3.553A pdb=" N GLU C3642 " --> pdb=" O ASP C3638 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.959A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 3.505A pdb=" N ALA C3675 " --> pdb=" O PHE C3671 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 4.019A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C3694 " --> pdb=" O ALA C3690 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C3695 " --> pdb=" O TYR C3691 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C3696 " --> pdb=" O ALA C3692 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C3697 " --> pdb=" O ASP C3693 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS C3699 " --> pdb=" O MET C3695 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C3701 " --> pdb=" O LYS C3697 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.554A pdb=" N LEU C3724 " --> pdb=" O GLU C3720 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.646A pdb=" N VAL C3740 " --> pdb=" O ALA C3736 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 removed outlier: 3.510A pdb=" N ALA C3757 " --> pdb=" O PRO C3753 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C3760 " --> pdb=" O ALA C3756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C3761 " --> pdb=" O ALA C3757 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C3763 " --> pdb=" O LEU C3759 " (cutoff:3.500A) Processing helix chain 'C' and resid 3770 through 3785 removed outlier: 3.512A pdb=" N LEU C3781 " --> pdb=" O MET C3777 " (cutoff:3.500A) Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.609A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C3800 " --> pdb=" O LEU C3796 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.764A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 4.001A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C3843 " --> pdb=" O LEU C3839 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.698A pdb=" N ASN C3856 " --> pdb=" O SER C3852 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR C3857 " --> pdb=" O ASP C3853 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 3.774A pdb=" N VAL C3875 " --> pdb=" O ILE C3871 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C3877 " --> pdb=" O SER C3873 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C3887 " --> pdb=" O GLU C3883 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 removed outlier: 3.677A pdb=" N ASN C3905 " --> pdb=" O GLN C3901 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C3906 " --> pdb=" O GLY C3902 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C3912 " --> pdb=" O LYS C3908 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C3924 " --> pdb=" O LEU C3920 " (cutoff:3.500A) Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 3.792A pdb=" N ALA C3936 " --> pdb=" O GLN C3932 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS C3937 " --> pdb=" O GLN C3933 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C3938 " --> pdb=" O SER C3934 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 3.565A pdb=" N GLY C3946 " --> pdb=" O ASP C3942 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS C3949 " --> pdb=" O VAL C3945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C3953 " --> pdb=" O HIS C3949 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN C3955 " --> pdb=" O PHE C3951 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.919A pdb=" N LEU C3968 " --> pdb=" O GLN C3964 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C3976 " --> pdb=" O MET C3972 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C3986 " --> pdb=" O LEU C3982 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C3987 " --> pdb=" O LEU C3983 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.567A pdb=" N PHE C4016 " --> pdb=" O MET C4012 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 removed outlier: 3.963A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.565A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.347A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 3.781A pdb=" N VAL C4084 " --> pdb=" O TYR C4080 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS C4085 " --> pdb=" O GLU C4081 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C4087 " --> pdb=" O PHE C4083 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C4088 " --> pdb=" O VAL C4084 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.128A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 4.200A pdb=" N GLU C4120 " --> pdb=" O GLN C4116 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU C4121 " --> pdb=" O THR C4117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C4122 " --> pdb=" O PHE C4118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C4123 " --> pdb=" O LEU C4119 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4131 removed outlier: 3.718A pdb=" N GLN C4130 " --> pdb=" O LEU C4126 " (cutoff:3.500A) Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4162 removed outlier: 3.508A pdb=" N LYS C4162 " --> pdb=" O THR C4158 " (cutoff:3.500A) Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4181 through 4208 removed outlier: 3.848A pdb=" N LYS C4185 " --> pdb=" O GLY C4181 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4258 removed outlier: 4.297A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4273 removed outlier: 4.392A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.770A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C4310 " --> pdb=" O PHE C4306 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.965A pdb=" N ILE C4485 " --> pdb=" O TRP C4481 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 3.885A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C4510 " --> pdb=" O ALA C4506 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C4518 " --> pdb=" O ASN C4514 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.138A 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: 3.962A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 removed outlier: 3.522A pdb=" N SER C4667 " --> pdb=" O ARG C4663 " (cutoff:3.500A) Processing helix chain 'C' and resid 4675 through 4683 Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.881A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.794A pdb=" N TYR C4721 " --> pdb=" O ASN C4717 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4750 removed outlier: 4.993A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4762 removed outlier: 4.412A pdb=" N THR C4755 " --> pdb=" O LYS C4751 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 removed outlier: 3.894A pdb=" N VAL C4768 " --> pdb=" O GLY C4764 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C4771 " --> pdb=" O LEU C4767 " (cutoff:3.500A) Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.352A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 5.236A 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: 3.727A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.765A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C4831 " --> pdb=" O ILE C4827 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4826 through 4832' Processing helix chain 'C' and resid 4839 through 4854 removed outlier: 3.793A pdb=" N ARG C4843 " --> pdb=" O TYR C4839 " (cutoff:3.500A) Processing helix chain 'C' and resid 4858 through 4887 removed outlier: 3.800A pdb=" N ILE C4862 " --> pdb=" O LEU C4858 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C4863 " --> pdb=" O LEU C4859 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C4871 " --> pdb=" O ILE C4867 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.894A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR C4900 " --> pdb=" O ASP C4896 " (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 removed outlier: 3.544A pdb=" N GLU C4963 " --> pdb=" O ARG C4959 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.026A pdb=" N ALA C 861 " --> pdb=" O THR C 858 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.725A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR C1776 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1772 through 1778' Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.864A pdb=" N ALA C 328 " --> pdb=" O ASP C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 328' Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 4.601A pdb=" N ILE C2382 " --> pdb=" O GLU C2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' Processing helix chain 'C' and resid 4614 through 4619 Processing sheet with id= 1, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.890A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'H' and resid 46 through 50 removed outlier: 3.583A pdb=" N GLU H 108 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.890A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 46 through 50 removed outlier: 3.584A pdb=" N GLU E 108 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.890A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'F' and resid 46 through 50 removed outlier: 3.583A pdb=" N GLU F 108 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.890A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 46 through 50 removed outlier: 3.584A pdb=" N GLU G 108 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.315A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.539A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 70 through 73 removed outlier: 3.671A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 160 through 163 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= 13, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.826A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 15, first strand: chain 'A' and resid 329 through 332 Processing sheet with id= 16, first strand: chain 'A' and resid 692 through 697 removed outlier: 5.626A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.992A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A1617 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.610A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.246A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 7.059A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 4.001A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A1091 " --> pdb=" O THR A1248 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 1267 through 1276 removed outlier: 6.707A pdb=" N ILE A1268 " --> pdb=" O GLN A1287 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN A1287 " --> pdb=" O ILE A1268 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1270 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1285 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG A1272 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A1283 " --> pdb=" O ARG A1272 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP A1274 " --> pdb=" O PRO A1281 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR A1276 " --> pdb=" O SER A1279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1283 " --> pdb=" O PHE A1555 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A1554 " --> pdb=" O ARG A1431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A1431 " --> pdb=" O GLN A1554 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.928A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'A' and resid 2746 through 2749 removed outlier: 7.419A pdb=" N ILE A2746 " --> pdb=" O PRO A2755 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.845A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.538A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.314A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.539A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 70 through 73 removed outlier: 3.671A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 160 through 163 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 31, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.826A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 33, first strand: chain 'D' and resid 329 through 332 Processing sheet with id= 34, first strand: chain 'D' and resid 692 through 697 removed outlier: 5.627A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.992A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D1617 " --> pdb=" O PHE D 802 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.610A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.246A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 7.058A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 4.001A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU D1091 " --> pdb=" O THR D1248 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 1267 through 1276 removed outlier: 6.706A pdb=" N ILE D1268 " --> pdb=" O GLN D1287 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN D1287 " --> pdb=" O ILE D1268 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL D1270 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D1285 " --> pdb=" O VAL D1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D1272 " --> pdb=" O LEU D1283 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU D1283 " --> pdb=" O ARG D1272 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP D1274 " --> pdb=" O PRO D1281 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR D1276 " --> pdb=" O SER D1279 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D1283 " --> pdb=" O PHE D1555 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D1554 " --> pdb=" O ARG D1431 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D1431 " --> pdb=" O GLN D1554 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.929A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 2746 through 2749 removed outlier: 7.419A pdb=" N ILE D2746 " --> pdb=" O PRO D2755 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.845A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.538A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.314A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.539A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 70 through 73 removed outlier: 3.671A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 160 through 163 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 49, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.827A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 51, first strand: chain 'B' and resid 329 through 332 Processing sheet with id= 52, first strand: chain 'B' and resid 692 through 697 removed outlier: 5.628A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.992A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B1617 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.609A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.246A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 7.058A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 4.001A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B1091 " --> pdb=" O THR B1248 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 1267 through 1276 removed outlier: 6.707A pdb=" N ILE B1268 " --> pdb=" O GLN B1287 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN B1287 " --> pdb=" O ILE B1268 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B1270 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B1285 " --> pdb=" O VAL B1270 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG B1272 " --> pdb=" O LEU B1283 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1283 " --> pdb=" O ARG B1272 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B1274 " --> pdb=" O PRO B1281 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B1276 " --> pdb=" O SER B1279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B1283 " --> pdb=" O PHE B1555 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B1554 " --> pdb=" O ARG B1431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B1431 " --> pdb=" O GLN B1554 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.928A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'B' and resid 2746 through 2749 removed outlier: 7.419A pdb=" N ILE B2746 " --> pdb=" O PRO B2755 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.844A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.539A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.315A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.539A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 70 through 73 removed outlier: 3.671A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'C' and resid 160 through 163 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 67, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.827A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 69, first strand: chain 'C' and resid 329 through 332 Processing sheet with id= 70, first strand: chain 'C' and resid 692 through 697 removed outlier: 5.627A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.993A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP C1617 " --> pdb=" O PHE C 802 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.610A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.245A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 7.058A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 4.001A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C1091 " --> pdb=" O THR C1248 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 1267 through 1276 removed outlier: 6.707A pdb=" N ILE C1268 " --> pdb=" O GLN C1287 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN C1287 " --> pdb=" O ILE C1268 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1270 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1285 " --> pdb=" O VAL C1270 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG C1272 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1283 " --> pdb=" O ARG C1272 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP C1274 " --> pdb=" O PRO C1281 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C1276 " --> pdb=" O SER C1279 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C1283 " --> pdb=" O PHE C1555 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C1554 " --> pdb=" O ARG C1431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C1431 " --> pdb=" O GLN C1554 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.928A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'C' and resid 2746 through 2749 removed outlier: 7.420A pdb=" N ILE C2746 " --> pdb=" O PRO C2755 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.844A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.538A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) 6330 hydrogen bonds defined for protein. 18842 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: 97.88 Time building geometry restraints manager: 47.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 45219 1.34 - 1.46: 32624 1.46 - 1.59: 62237 1.59 - 1.71: 36 1.71 - 1.84: 1512 Bond restraints: 141628 Sorted by residual: bond pdb=" CG LYS D2736 " pdb=" CD LYS D2736 " ideal model delta sigma weight residual 1.520 1.422 0.098 3.00e-02 1.11e+03 1.07e+01 bond pdb=" CG LYS B2736 " pdb=" CD LYS B2736 " ideal model delta sigma weight residual 1.520 1.422 0.098 3.00e-02 1.11e+03 1.06e+01 bond pdb=" CG LYS C2736 " pdb=" CD LYS C2736 " ideal model delta sigma weight residual 1.520 1.422 0.098 3.00e-02 1.11e+03 1.06e+01 bond pdb=" CG LYS A2736 " pdb=" CD LYS A2736 " ideal model delta sigma weight residual 1.520 1.423 0.097 3.00e-02 1.11e+03 1.05e+01 bond pdb=" C GLY A4662 " pdb=" N ARG A4663 " ideal model delta sigma weight residual 1.332 1.376 -0.043 1.40e-02 5.10e+03 9.61e+00 ... (remaining 141623 not shown) Histogram of bond angle deviations from ideal: 93.90 - 103.09: 1407 103.09 - 112.28: 68773 112.28 - 121.46: 85541 121.46 - 130.65: 34848 130.65 - 139.84: 787 Bond angle restraints: 191356 Sorted by residual: angle pdb=" C VAL C1563 " pdb=" N MET C1564 " pdb=" CA MET C1564 " ideal model delta sigma weight residual 120.67 136.52 -15.85 1.34e+00 5.57e-01 1.40e+02 angle pdb=" C VAL B1563 " pdb=" N MET B1564 " pdb=" CA MET B1564 " ideal model delta sigma weight residual 120.67 136.50 -15.83 1.34e+00 5.57e-01 1.40e+02 angle pdb=" C VAL D1563 " pdb=" N MET D1564 " pdb=" CA MET D1564 " ideal model delta sigma weight residual 120.67 136.48 -15.81 1.34e+00 5.57e-01 1.39e+02 angle pdb=" C VAL A1563 " pdb=" N MET A1564 " pdb=" CA MET A1564 " ideal model delta sigma weight residual 120.67 136.48 -15.81 1.34e+00 5.57e-01 1.39e+02 angle pdb=" CA GLU F 4 " pdb=" CB GLU F 4 " pdb=" CG GLU F 4 " ideal model delta sigma weight residual 114.10 131.72 -17.62 2.00e+00 2.50e-01 7.76e+01 ... (remaining 191351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 77233 17.95 - 35.90: 6565 35.90 - 53.86: 1156 53.86 - 71.81: 346 71.81 - 89.76: 112 Dihedral angle restraints: 85412 sinusoidal: 35052 harmonic: 50360 Sorted by residual: 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 -138.93 -41.07 0 5.00e+00 4.00e-02 6.75e+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 -138.96 -41.04 0 5.00e+00 4.00e-02 6.74e+01 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 -138.96 -41.04 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 85409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 18611 0.065 - 0.131: 2259 0.131 - 0.196: 83 0.196 - 0.261: 27 0.261 - 0.326: 8 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE D3122 " pdb=" CA ILE D3122 " pdb=" CG1 ILE D3122 " pdb=" CG2 ILE D3122 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE C3122 " pdb=" CA ILE C3122 " pdb=" CG1 ILE C3122 " pdb=" CG2 ILE C3122 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE B3122 " pdb=" CA ILE B3122 " pdb=" CG1 ILE B3122 " pdb=" CG2 ILE B3122 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " -0.119 5.00e-02 4.00e+02 1.83e-01 5.36e+01 pdb=" N PRO C4641 " 0.316 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " -0.109 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " 0.119 5.00e-02 4.00e+02 1.83e-01 5.36e+01 pdb=" N PRO B4641 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.119 5.00e-02 4.00e+02 1.83e-01 5.35e+01 pdb=" N PRO A4641 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.088 5.00e-02 4.00e+02 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1630 2.63 - 3.20: 126226 3.20 - 3.77: 223099 3.77 - 4.33: 314676 4.33 - 4.90: 500668 Nonbonded interactions: 1166299 Sorted by model distance: nonbonded pdb=" N GLU A4797 " pdb=" OE1 GLU A4797 " model vdw 2.065 2.520 nonbonded pdb=" N GLU D4797 " pdb=" OE1 GLU D4797 " model vdw 2.065 2.520 nonbonded pdb=" N GLU B4797 " pdb=" OE1 GLU B4797 " model vdw 2.065 2.520 nonbonded pdb=" N GLU C4797 " pdb=" OE1 GLU C4797 " model vdw 2.066 2.520 nonbonded pdb=" OG SER B4622 " pdb=" OD1 ASP B4624 " model vdw 2.131 2.440 ... (remaining 1166294 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 31.330 Check model and map are aligned: 1.570 Set scattering table: 0.970 Process input model: 453.980 Find NCS groups from input model: 8.010 Set up NCS constraints: 1.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 506.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 0.098 141628 Z= 0.203 Angle : 0.848 19.136 191356 Z= 0.492 Chirality : 0.043 0.326 20988 Planarity : 0.006 0.183 24588 Dihedral : 14.305 89.760 52936 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 0.66 % Allowed : 0.84 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.06), residues: 17212 helix: -0.69 (0.06), residues: 8568 sheet: -0.58 (0.12), residues: 1676 loop : -0.92 (0.07), residues: 6968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C2732 HIS 0.010 0.001 HIS D3252 PHE 0.028 0.001 PHE A2943 TYR 0.060 0.002 TYR B4567 ARG 0.026 0.001 ARG A1009 *********************** 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 982 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 890 time to evaluate : 12.717 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: H 19 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8539 (mmmm) REVERT: H 45 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8760 (mtmm) REVERT: H 53 LYS cc_start: 0.9187 (mmtp) cc_final: 0.8795 (mmtp) REVERT: A 399 MET cc_start: 0.7510 (tmm) cc_final: 0.7280 (tmm) REVERT: A 940 LEU cc_start: 0.9390 (mt) cc_final: 0.9158 (mt) REVERT: A 956 HIS cc_start: 0.9010 (t70) cc_final: 0.8740 (t70) REVERT: A 1113 MET cc_start: 0.8001 (mtp) cc_final: 0.7759 (mtp) REVERT: A 1173 MET cc_start: 0.8113 (mtt) cc_final: 0.7770 (mtp) REVERT: A 2142 MET cc_start: 0.8341 (tpt) cc_final: 0.8001 (tpp) REVERT: A 2347 MET cc_start: 0.7506 (mmp) cc_final: 0.7170 (mmp) REVERT: A 2553 TYR cc_start: 0.7525 (t80) cc_final: 0.6901 (t80) REVERT: A 2719 TYR cc_start: 0.8607 (t80) cc_final: 0.8385 (t80) REVERT: A 2720 PHE cc_start: 0.8475 (t80) cc_final: 0.8166 (t80) REVERT: A 2724 TYR cc_start: 0.8656 (t80) cc_final: 0.8089 (t80) REVERT: A 2782 MET cc_start: 0.8363 (ppp) cc_final: 0.8092 (ppp) REVERT: A 2783 LEU cc_start: 0.9474 (mt) cc_final: 0.9209 (mt) REVERT: A 2892 ILE cc_start: 0.9151 (tt) cc_final: 0.8950 (tp) REVERT: A 2932 TYR cc_start: 0.8373 (t80) cc_final: 0.8064 (t80) REVERT: A 2963 PHE cc_start: 0.8391 (t80) cc_final: 0.8026 (t80) REVERT: A 3022 PHE cc_start: 0.8134 (m-10) cc_final: 0.7752 (m-10) REVERT: A 4032 PHE cc_start: 0.8818 (t80) cc_final: 0.8504 (t80) REVERT: A 4748 MET cc_start: 0.6802 (mpp) cc_final: 0.6278 (mpp) REVERT: G 51 ILE cc_start: 0.9241 (mm) cc_final: 0.8983 (mt) REVERT: D 778 MET cc_start: 0.7933 (ptm) cc_final: 0.7564 (ptm) REVERT: D 940 LEU cc_start: 0.9302 (mt) cc_final: 0.9059 (mt) REVERT: D 956 HIS cc_start: 0.9041 (t70) cc_final: 0.8770 (t70) REVERT: D 1165 MET cc_start: 0.7829 (mtp) cc_final: 0.7537 (mtp) REVERT: D 1173 MET cc_start: 0.7904 (mtt) cc_final: 0.7582 (mtp) REVERT: D 1174 MET cc_start: 0.7573 (mtp) cc_final: 0.7308 (mtm) REVERT: D 1300 MET cc_start: 0.8188 (mmm) cc_final: 0.7791 (mmm) REVERT: D 2142 MET cc_start: 0.8421 (tpt) cc_final: 0.7960 (tpp) REVERT: D 2689 MET cc_start: 0.3073 (ptp) cc_final: 0.2825 (ptp) REVERT: D 2695 MET cc_start: 0.5936 (pmm) cc_final: 0.5711 (pmm) REVERT: D 2719 TYR cc_start: 0.8672 (t80) cc_final: 0.8367 (t80) REVERT: D 2720 PHE cc_start: 0.8553 (t80) cc_final: 0.8005 (t80) REVERT: D 2731 LYS cc_start: 0.9248 (mtmm) cc_final: 0.8999 (ptpt) REVERT: D 2771 TYR cc_start: 0.8157 (m-80) cc_final: 0.7863 (m-10) REVERT: D 2782 MET cc_start: 0.8214 (ppp) cc_final: 0.7939 (ppp) REVERT: D 2783 LEU cc_start: 0.9334 (mt) cc_final: 0.8853 (mt) REVERT: D 2826 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7434 (tt) REVERT: D 2932 TYR cc_start: 0.8506 (t80) cc_final: 0.8268 (t80) REVERT: D 3134 LEU cc_start: 0.9186 (mt) cc_final: 0.8949 (mt) REVERT: D 3263 MET cc_start: 0.7623 (pmm) cc_final: 0.7263 (pmm) REVERT: D 3318 HIS cc_start: 0.8179 (p-80) cc_final: 0.7962 (p90) REVERT: D 3319 PHE cc_start: 0.8198 (m-80) cc_final: 0.7951 (m-80) REVERT: B 399 MET cc_start: 0.7465 (tmm) cc_final: 0.7235 (tmm) REVERT: B 940 LEU cc_start: 0.9334 (mt) cc_final: 0.9044 (mt) REVERT: B 956 HIS cc_start: 0.9137 (t70) cc_final: 0.8882 (t70) REVERT: B 1035 TYR cc_start: 0.7158 (t80) cc_final: 0.6635 (t80) REVERT: B 1165 MET cc_start: 0.7939 (mtp) cc_final: 0.7627 (mtp) REVERT: B 1168 MET cc_start: 0.8446 (mmm) cc_final: 0.7565 (mmm) REVERT: B 2142 MET cc_start: 0.8312 (tpt) cc_final: 0.8073 (tpt) REVERT: B 2248 MET cc_start: 0.7697 (ttm) cc_final: 0.7355 (ttm) REVERT: B 2347 MET cc_start: 0.7604 (mmp) cc_final: 0.7324 (mmp) REVERT: B 2681 MET cc_start: 0.8869 (tpt) cc_final: 0.8600 (tpt) REVERT: B 2689 MET cc_start: 0.3263 (ptp) cc_final: 0.2907 (ptm) REVERT: B 2720 PHE cc_start: 0.8580 (t80) cc_final: 0.8272 (t80) REVERT: B 2826 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7529 (tt) REVERT: B 2844 MET cc_start: 0.8874 (ppp) cc_final: 0.8605 (ppp) REVERT: B 2932 TYR cc_start: 0.8244 (t80) cc_final: 0.8006 (t80) REVERT: B 2963 PHE cc_start: 0.8244 (t80) cc_final: 0.8010 (t80) REVERT: B 4139 MET cc_start: 0.8088 (tpp) cc_final: 0.7631 (tpt) REVERT: B 4274 MET cc_start: 0.5513 (ttt) cc_final: 0.5036 (ptp) REVERT: B 4726 MET cc_start: 0.7827 (tpt) cc_final: 0.7405 (tpt) REVERT: C 399 MET cc_start: 0.7474 (tmm) cc_final: 0.7221 (tmm) REVERT: C 778 MET cc_start: 0.7521 (ptm) cc_final: 0.7226 (ptm) REVERT: C 956 HIS cc_start: 0.9249 (t70) cc_final: 0.8987 (t70) REVERT: C 1300 MET cc_start: 0.8169 (mmm) cc_final: 0.7910 (mmt) REVERT: C 2066 MET cc_start: 0.8574 (mmt) cc_final: 0.8109 (mmm) REVERT: C 2142 MET cc_start: 0.8584 (tpt) cc_final: 0.8266 (tpp) REVERT: C 2688 MET cc_start: 0.2748 (ptt) cc_final: 0.2468 (ptt) REVERT: C 2719 TYR cc_start: 0.8600 (t80) cc_final: 0.8335 (t80) REVERT: C 2720 PHE cc_start: 0.8677 (t80) cc_final: 0.8357 (t80) REVERT: C 2724 TYR cc_start: 0.8763 (t80) cc_final: 0.8067 (t80) REVERT: C 2731 LYS cc_start: 0.9356 (mtmm) cc_final: 0.8689 (pttm) REVERT: C 2844 MET cc_start: 0.9003 (ppp) cc_final: 0.8657 (ppp) REVERT: C 2932 TYR cc_start: 0.8523 (t80) cc_final: 0.8119 (t80) REVERT: C 2963 PHE cc_start: 0.8328 (t80) cc_final: 0.8081 (t80) REVERT: C 3022 PHE cc_start: 0.8331 (m-10) cc_final: 0.8034 (m-10) REVERT: C 3104 MET cc_start: 0.8525 (ppp) cc_final: 0.8311 (ppp) REVERT: C 3131 TYR cc_start: 0.8503 (m-10) cc_final: 0.8024 (m-10) REVERT: C 3263 MET cc_start: 0.7472 (pmm) cc_final: 0.7078 (pmm) REVERT: C 3319 PHE cc_start: 0.8237 (m-80) cc_final: 0.7990 (m-80) REVERT: C 4726 MET cc_start: 0.8258 (tpt) cc_final: 0.7713 (tpt) outliers start: 92 outliers final: 24 residues processed: 921 average time/residue: 1.2282 time to fit residues: 1981.3617 Evaluate side-chains 806 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 779 time to evaluate : 10.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 4797 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 1564 MET Chi-restraints excluded: chain D residue 2485 LEU Chi-restraints excluded: chain D residue 2826 ILE Chi-restraints excluded: chain D residue 4797 GLU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 1564 MET Chi-restraints excluded: chain B residue 2826 ILE Chi-restraints excluded: chain B residue 4797 GLU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 1564 MET Chi-restraints excluded: chain C residue 2485 LEU Chi-restraints excluded: chain C residue 4797 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 10.0000 chunk 1309 optimal weight: 2.9990 chunk 726 optimal weight: 8.9990 chunk 447 optimal weight: 10.0000 chunk 883 optimal weight: 0.7980 chunk 699 optimal weight: 10.0000 chunk 1354 optimal weight: 9.9990 chunk 524 optimal weight: 10.0000 chunk 823 optimal weight: 6.9990 chunk 1008 optimal weight: 10.0000 chunk 1569 optimal weight: 20.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN A2316 ASN ** A2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2613 HIS ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3127 GLN ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3274 ASN ** A3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 HIS A4742 HIS ** A4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS G 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 HIS ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2316 ASN ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2541 HIS D2550 HIS ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3127 GLN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3274 ASN D4088 HIS ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 HIS ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 GLN ** B2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3274 ASN ** B3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 HIS ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN C1836 ASN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2550 HIS ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3127 GLN ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3274 ASN C4088 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 141628 Z= 0.417 Angle : 0.731 14.890 191356 Z= 0.378 Chirality : 0.045 0.292 20988 Planarity : 0.006 0.157 24588 Dihedral : 6.731 92.951 19106 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 0.50 % Allowed : 4.05 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.06), residues: 17212 helix: -0.05 (0.06), residues: 8736 sheet: -0.52 (0.12), residues: 1796 loop : -0.77 (0.07), residues: 6680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C4481 HIS 0.012 0.002 HIS D2849 PHE 0.043 0.002 PHE D2895 TYR 0.047 0.002 TYR D2939 ARG 0.017 0.001 ARG A1009 *********************** 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 917 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 849 time to evaluate : 12.486 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: H 45 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8796 (mtmm) REVERT: H 51 ILE cc_start: 0.9259 (mm) cc_final: 0.8847 (mm) REVERT: A 81 MET cc_start: 0.8270 (tmm) cc_final: 0.7759 (tmm) REVERT: A 399 MET cc_start: 0.7609 (tmm) cc_final: 0.7379 (tmm) REVERT: A 940 LEU cc_start: 0.9453 (mt) cc_final: 0.9249 (mt) REVERT: A 956 HIS cc_start: 0.9061 (t70) cc_final: 0.8781 (t70) REVERT: A 1113 MET cc_start: 0.8302 (mtp) cc_final: 0.8063 (mtm) REVERT: A 1487 MET cc_start: 0.8838 (mtm) cc_final: 0.8546 (mtt) REVERT: A 1494 MET cc_start: 0.7696 (tmm) cc_final: 0.7380 (tmm) REVERT: A 1975 MET cc_start: 0.8448 (ppp) cc_final: 0.8231 (ppp) REVERT: A 2347 MET cc_start: 0.7739 (mmp) cc_final: 0.7350 (mmp) REVERT: A 2493 LEU cc_start: 0.9055 (mm) cc_final: 0.8813 (mp) REVERT: A 2553 TYR cc_start: 0.7752 (t80) cc_final: 0.7142 (t80) REVERT: A 2585 MET cc_start: 0.8097 (mpp) cc_final: 0.7771 (pmm) REVERT: A 2681 MET cc_start: 0.8475 (tpt) cc_final: 0.7773 (mmm) REVERT: A 2695 MET cc_start: 0.6169 (pmm) cc_final: 0.5893 (pmm) REVERT: A 2719 TYR cc_start: 0.8593 (t80) cc_final: 0.8373 (t80) REVERT: A 2720 PHE cc_start: 0.8562 (t80) cc_final: 0.8159 (t80) REVERT: A 2724 TYR cc_start: 0.8638 (t80) cc_final: 0.8420 (t80) REVERT: A 2734 MET cc_start: 0.6788 (mmm) cc_final: 0.6479 (ptp) REVERT: A 2828 MET cc_start: 0.6732 (pmm) cc_final: 0.6221 (pmm) REVERT: A 2932 TYR cc_start: 0.8430 (t80) cc_final: 0.8083 (t80) REVERT: A 2963 PHE cc_start: 0.8453 (t80) cc_final: 0.8030 (t80) REVERT: A 3022 PHE cc_start: 0.8251 (m-10) cc_final: 0.7796 (m-10) REVERT: A 3072 MET cc_start: 0.8893 (mmp) cc_final: 0.8513 (mmm) REVERT: A 3104 MET cc_start: 0.8436 (ppp) cc_final: 0.8209 (ppp) REVERT: A 3273 MET cc_start: 0.9423 (ppp) cc_final: 0.9103 (ppp) REVERT: A 3323 MET cc_start: 0.8204 (mmt) cc_final: 0.7951 (mmt) REVERT: A 3605 MET cc_start: 0.7016 (tmm) cc_final: 0.6787 (tmm) REVERT: A 3978 MET cc_start: 0.8917 (ttp) cc_final: 0.8666 (ttp) REVERT: A 3981 MET cc_start: 0.8873 (tmm) cc_final: 0.8465 (tmm) REVERT: A 4032 PHE cc_start: 0.8865 (t80) cc_final: 0.8663 (t80) REVERT: A 4268 MET cc_start: 0.6036 (tmm) cc_final: 0.5708 (tmm) REVERT: E 106 ASN cc_start: 0.8770 (t0) cc_final: 0.8309 (t0) REVERT: F 18 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8464 (mtmm) REVERT: D 81 MET cc_start: 0.8402 (tmm) cc_final: 0.8124 (tmm) REVERT: D 778 MET cc_start: 0.8084 (ptm) cc_final: 0.7674 (ptm) REVERT: D 940 LEU cc_start: 0.9379 (mt) cc_final: 0.9145 (mt) REVERT: D 956 HIS cc_start: 0.9062 (t70) cc_final: 0.8790 (t70) REVERT: D 1300 MET cc_start: 0.8434 (mmm) cc_final: 0.7961 (mmm) REVERT: D 1487 MET cc_start: 0.8830 (mtp) cc_final: 0.8487 (mtt) REVERT: D 1494 MET cc_start: 0.7632 (tmm) cc_final: 0.7163 (tmm) REVERT: D 2142 MET cc_start: 0.8482 (tpt) cc_final: 0.8086 (tpp) REVERT: D 2534 LEU cc_start: 0.9061 (mt) cc_final: 0.8659 (tp) REVERT: D 2540 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7486 (p-80) REVERT: D 2584 MET cc_start: 0.8403 (mtm) cc_final: 0.7898 (mpp) REVERT: D 2681 MET cc_start: 0.8275 (tpt) cc_final: 0.7360 (mmm) REVERT: D 2719 TYR cc_start: 0.8702 (t80) cc_final: 0.8421 (t80) REVERT: D 2771 TYR cc_start: 0.8500 (m-80) cc_final: 0.8006 (m-10) REVERT: D 2783 LEU cc_start: 0.9300 (mt) cc_final: 0.9043 (mt) REVERT: D 2932 TYR cc_start: 0.8604 (t80) cc_final: 0.8281 (t80) REVERT: D 3072 MET cc_start: 0.8859 (mmm) cc_final: 0.8493 (mmm) REVERT: D 3134 LEU cc_start: 0.9229 (mt) cc_final: 0.9017 (mt) REVERT: D 3184 TYR cc_start: 0.8613 (m-10) cc_final: 0.8399 (m-10) REVERT: D 3318 HIS cc_start: 0.8230 (p-80) cc_final: 0.7882 (p90) REVERT: D 3319 PHE cc_start: 0.8233 (m-80) cc_final: 0.7935 (m-80) REVERT: D 3978 MET cc_start: 0.8911 (ttp) cc_final: 0.8665 (ttp) REVERT: D 4186 MET cc_start: 0.8931 (mmt) cc_final: 0.8636 (mmt) REVERT: B 393 MET cc_start: 0.6517 (mtm) cc_final: 0.6267 (mtm) REVERT: B 399 MET cc_start: 0.7546 (tmm) cc_final: 0.7263 (tmm) REVERT: B 940 LEU cc_start: 0.9415 (mt) cc_final: 0.9165 (mt) REVERT: B 956 HIS cc_start: 0.9175 (t70) cc_final: 0.8920 (t70) REVERT: B 1035 TYR cc_start: 0.7455 (t80) cc_final: 0.6905 (t80) REVERT: B 1113 MET cc_start: 0.8075 (mtm) cc_final: 0.7717 (mtp) REVERT: B 1165 MET cc_start: 0.7894 (mtp) cc_final: 0.7423 (mtp) REVERT: B 1168 MET cc_start: 0.8628 (mmm) cc_final: 0.8386 (mmm) REVERT: B 1906 MET cc_start: 0.8254 (mmm) cc_final: 0.7907 (mmm) REVERT: B 1975 MET cc_start: 0.9025 (ptt) cc_final: 0.8716 (ppp) REVERT: B 2347 MET cc_start: 0.7853 (mmp) cc_final: 0.7445 (mmp) REVERT: B 2384 MET cc_start: 0.8530 (mpp) cc_final: 0.8180 (mpp) REVERT: B 2585 MET cc_start: 0.7857 (mpp) cc_final: 0.7483 (pmm) REVERT: B 2669 LEU cc_start: 0.9076 (mt) cc_final: 0.8793 (mt) REVERT: B 2688 MET cc_start: 0.1927 (ptt) cc_final: 0.1688 (ptt) REVERT: B 2720 PHE cc_start: 0.8615 (t80) cc_final: 0.8226 (t80) REVERT: B 2724 TYR cc_start: 0.8479 (t80) cc_final: 0.8184 (t80) REVERT: B 2826 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 2932 TYR cc_start: 0.8277 (t80) cc_final: 0.7973 (t80) REVERT: B 2963 PHE cc_start: 0.8318 (t80) cc_final: 0.8019 (t80) REVERT: B 3046 MET cc_start: 0.7501 (mmp) cc_final: 0.7242 (mmm) REVERT: B 3109 PHE cc_start: 0.8788 (m-10) cc_final: 0.8467 (m-10) REVERT: B 3318 HIS cc_start: 0.8300 (p90) cc_final: 0.7975 (p-80) REVERT: B 4048 PHE cc_start: 0.8654 (m-80) cc_final: 0.8371 (m-80) REVERT: B 4052 MET cc_start: 0.8555 (mtp) cc_final: 0.8110 (ttm) REVERT: B 4268 MET cc_start: 0.6394 (tmm) cc_final: 0.6168 (tmm) REVERT: B 4274 MET cc_start: 0.5407 (ttt) cc_final: 0.4748 (ptm) REVERT: B 4726 MET cc_start: 0.8392 (tpt) cc_final: 0.8167 (tpt) REVERT: C 81 MET cc_start: 0.8290 (tmm) cc_final: 0.7833 (tmm) REVERT: C 399 MET cc_start: 0.7558 (tmm) cc_final: 0.7285 (tmm) REVERT: C 956 HIS cc_start: 0.9266 (t70) cc_final: 0.9020 (t70) REVERT: C 995 MET cc_start: 0.8478 (mpp) cc_final: 0.8203 (mpp) REVERT: C 1249 MET cc_start: 0.7940 (mmm) cc_final: 0.7665 (mmm) REVERT: C 1487 MET cc_start: 0.8862 (mtp) cc_final: 0.8564 (mtt) REVERT: C 1694 MET cc_start: 0.8965 (tpp) cc_final: 0.8632 (tpp) REVERT: C 2142 MET cc_start: 0.8478 (tpt) cc_final: 0.8243 (tpp) REVERT: C 2279 MET cc_start: 0.8645 (ptm) cc_final: 0.8420 (tmm) REVERT: C 2384 MET cc_start: 0.8504 (mpp) cc_final: 0.8184 (mpp) REVERT: C 2669 LEU cc_start: 0.9261 (mt) cc_final: 0.9002 (mt) REVERT: C 2681 MET cc_start: 0.8795 (tpt) cc_final: 0.8491 (tpt) REVERT: C 2719 TYR cc_start: 0.8644 (t80) cc_final: 0.8361 (t80) REVERT: C 2720 PHE cc_start: 0.8727 (t80) cc_final: 0.8325 (t80) REVERT: C 2724 TYR cc_start: 0.8693 (t80) cc_final: 0.8459 (t80) REVERT: C 2840 MET cc_start: 0.9001 (ptm) cc_final: 0.8578 (mmm) REVERT: C 2843 MET cc_start: 0.8099 (ppp) cc_final: 0.7709 (ppp) REVERT: C 2932 TYR cc_start: 0.8571 (t80) cc_final: 0.8144 (t80) REVERT: C 2963 PHE cc_start: 0.8424 (t80) cc_final: 0.8189 (t80) REVERT: C 3022 PHE cc_start: 0.8392 (m-10) cc_final: 0.7997 (m-10) REVERT: C 3131 TYR cc_start: 0.8537 (m-10) cc_final: 0.8049 (m-10) REVERT: C 3159 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 3285 TYR cc_start: 0.7336 (m-10) cc_final: 0.6993 (m-80) REVERT: C 3296 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9099 (pmm) REVERT: C 3319 PHE cc_start: 0.8346 (m-80) cc_final: 0.8068 (m-80) REVERT: C 3819 MET cc_start: 0.6249 (ptp) cc_final: 0.6047 (ptp) REVERT: C 4048 PHE cc_start: 0.8752 (m-80) cc_final: 0.8447 (m-80) REVERT: C 4726 MET cc_start: 0.8477 (tpt) cc_final: 0.8190 (tpt) REVERT: C 4748 MET cc_start: 0.7189 (mpp) cc_final: 0.6760 (mpp) outliers start: 68 outliers final: 29 residues processed: 870 average time/residue: 1.1887 time to fit residues: 1826.4547 Evaluate side-chains 832 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 799 time to evaluate : 12.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2826 ILE Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1794 MET Chi-restraints excluded: chain B residue 2512 MET Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 2826 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2512 MET Chi-restraints excluded: chain C residue 3159 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.8980 chunk 487 optimal weight: 8.9990 chunk 1306 optimal weight: 0.8980 chunk 1068 optimal weight: 9.9990 chunk 432 optimal weight: 8.9990 chunk 1572 optimal weight: 50.0000 chunk 1698 optimal weight: 9.9990 chunk 1400 optimal weight: 9.9990 chunk 1558 optimal weight: 7.9990 chunk 535 optimal weight: 1.9990 chunk 1261 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2867 ASN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2867 ASN ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3127 GLN ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN C2316 ASN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2540 HIS ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2867 ASN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 141628 Z= 0.264 Angle : 0.632 15.250 191356 Z= 0.321 Chirality : 0.042 0.334 20988 Planarity : 0.005 0.145 24588 Dihedral : 6.068 73.801 19030 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 0.60 % Allowed : 5.41 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.06), residues: 17212 helix: 0.38 (0.06), residues: 8740 sheet: -0.36 (0.12), residues: 1732 loop : -0.72 (0.07), residues: 6740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A2787 HIS 0.010 0.001 HIS G 26 PHE 0.035 0.002 PHE D3170 TYR 0.039 0.002 TYR D2939 ARG 0.015 0.001 ARG C3298 *********************** 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 898 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 815 time to evaluate : 12.290 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: A 81 MET cc_start: 0.8260 (tmm) cc_final: 0.7752 (tmm) REVERT: A 399 MET cc_start: 0.7574 (tmm) cc_final: 0.7319 (tmm) REVERT: A 940 LEU cc_start: 0.9426 (mt) cc_final: 0.9210 (mt) REVERT: A 956 HIS cc_start: 0.9057 (t70) cc_final: 0.8779 (t70) REVERT: A 1113 MET cc_start: 0.8260 (mtp) cc_final: 0.7937 (mtm) REVERT: A 1165 MET cc_start: 0.8219 (mtp) cc_final: 0.7642 (mtm) REVERT: A 1249 MET cc_start: 0.7951 (tpp) cc_final: 0.7700 (tpt) REVERT: A 1487 MET cc_start: 0.8839 (mtm) cc_final: 0.8610 (mtp) REVERT: A 1494 MET cc_start: 0.7690 (tmm) cc_final: 0.7344 (tmm) REVERT: A 1694 MET cc_start: 0.8986 (tpp) cc_final: 0.8537 (tpp) REVERT: A 1906 MET cc_start: 0.8426 (mmm) cc_final: 0.8030 (mmm) REVERT: A 2142 MET cc_start: 0.8366 (tpt) cc_final: 0.8081 (tpp) REVERT: A 2347 MET cc_start: 0.7822 (mmp) cc_final: 0.7438 (mmp) REVERT: A 2406 MET cc_start: 0.7076 (tmm) cc_final: 0.6822 (tmm) REVERT: A 2493 LEU cc_start: 0.9033 (mm) cc_final: 0.8804 (mp) REVERT: A 2553 TYR cc_start: 0.7707 (t80) cc_final: 0.7080 (t80) REVERT: A 2681 MET cc_start: 0.8512 (tpt) cc_final: 0.8282 (tpt) REVERT: A 2695 MET cc_start: 0.6517 (pmm) cc_final: 0.6174 (pmm) REVERT: A 2719 TYR cc_start: 0.8585 (t80) cc_final: 0.8327 (t80) REVERT: A 2720 PHE cc_start: 0.8501 (t80) cc_final: 0.8113 (t80) REVERT: A 2724 TYR cc_start: 0.8575 (t80) cc_final: 0.8233 (t80) REVERT: A 2734 MET cc_start: 0.6918 (mmm) cc_final: 0.6491 (ptp) REVERT: A 2828 MET cc_start: 0.6756 (pmm) cc_final: 0.6138 (pmm) REVERT: A 2867 ASN cc_start: 0.0965 (OUTLIER) cc_final: -0.0797 (m-40) REVERT: A 2932 TYR cc_start: 0.8395 (t80) cc_final: 0.8049 (t80) REVERT: A 2963 PHE cc_start: 0.8409 (t80) cc_final: 0.7948 (t80) REVERT: A 3022 PHE cc_start: 0.8227 (m-10) cc_final: 0.7769 (m-10) REVERT: A 3104 MET cc_start: 0.8443 (ppp) cc_final: 0.8203 (ppp) REVERT: A 3249 TRP cc_start: 0.7831 (m100) cc_final: 0.7613 (m100) REVERT: A 3263 MET cc_start: 0.8086 (tmm) cc_final: 0.7810 (tpt) REVERT: A 3283 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8065 (tp) REVERT: A 3296 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8913 (pmm) REVERT: A 3981 MET cc_start: 0.8873 (tmm) cc_final: 0.8465 (tmm) REVERT: A 4268 MET cc_start: 0.6039 (tmm) cc_final: 0.5733 (tmm) REVERT: A 4292 MET cc_start: 0.8307 (mmm) cc_final: 0.7986 (mmm) REVERT: D 81 MET cc_start: 0.8386 (tmm) cc_final: 0.8068 (tmm) REVERT: D 778 MET cc_start: 0.8104 (ptm) cc_final: 0.7642 (ptm) REVERT: D 956 HIS cc_start: 0.9064 (t70) cc_final: 0.8788 (t70) REVERT: D 1249 MET cc_start: 0.7974 (tpp) cc_final: 0.7734 (tpt) REVERT: D 1487 MET cc_start: 0.8849 (mtp) cc_final: 0.8615 (mtt) REVERT: D 1494 MET cc_start: 0.7676 (tmm) cc_final: 0.7184 (tmm) REVERT: D 1906 MET cc_start: 0.8479 (mmm) cc_final: 0.8067 (mmm) REVERT: D 2084 MET cc_start: 0.8835 (mtp) cc_final: 0.8582 (mtm) REVERT: D 2142 MET cc_start: 0.8468 (tpt) cc_final: 0.8216 (tpt) REVERT: D 2534 LEU cc_start: 0.9058 (mt) cc_final: 0.8663 (tp) REVERT: D 2540 HIS cc_start: 0.7503 (p-80) cc_final: 0.7149 (p-80) REVERT: D 2584 MET cc_start: 0.8311 (mtm) cc_final: 0.7927 (mpp) REVERT: D 2688 MET cc_start: 0.1124 (ptt) cc_final: 0.0588 (ptt) REVERT: D 2719 TYR cc_start: 0.8698 (t80) cc_final: 0.8390 (t80) REVERT: D 2720 PHE cc_start: 0.8573 (t80) cc_final: 0.8133 (t80) REVERT: D 2724 TYR cc_start: 0.8828 (t80) cc_final: 0.8539 (t80) REVERT: D 2771 TYR cc_start: 0.8460 (m-80) cc_final: 0.7907 (m-10) REVERT: D 2782 MET cc_start: 0.8146 (ppp) cc_final: 0.7946 (ppp) REVERT: D 2783 LEU cc_start: 0.9324 (mt) cc_final: 0.8921 (mt) REVERT: D 2844 MET cc_start: 0.8658 (ppp) cc_final: 0.8454 (ppp) REVERT: D 2932 TYR cc_start: 0.8598 (t80) cc_final: 0.8261 (t80) REVERT: D 3072 MET cc_start: 0.8868 (mmm) cc_final: 0.8488 (mmm) REVERT: D 3134 LEU cc_start: 0.9244 (mt) cc_final: 0.8966 (mt) REVERT: D 3283 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8493 (tp) REVERT: D 3296 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9039 (pmm) REVERT: D 3819 MET cc_start: 0.6753 (ptp) cc_final: 0.6388 (ptp) REVERT: D 4748 MET cc_start: 0.7138 (mpp) cc_final: 0.6926 (mpp) REVERT: B 81 MET cc_start: 0.8081 (tmm) cc_final: 0.7732 (tmm) REVERT: B 399 MET cc_start: 0.7520 (tmm) cc_final: 0.7153 (tmm) REVERT: B 940 LEU cc_start: 0.9382 (mt) cc_final: 0.9116 (mt) REVERT: B 956 HIS cc_start: 0.9171 (t70) cc_final: 0.8919 (t70) REVERT: B 1035 TYR cc_start: 0.7424 (t80) cc_final: 0.6908 (t80) REVERT: B 1113 MET cc_start: 0.8052 (mtm) cc_final: 0.7728 (mtp) REVERT: B 1165 MET cc_start: 0.8045 (mtp) cc_final: 0.7643 (mtp) REVERT: B 1168 MET cc_start: 0.8602 (mmm) cc_final: 0.8334 (mmm) REVERT: B 1906 MET cc_start: 0.8250 (mmm) cc_final: 0.7970 (mmm) REVERT: B 2162 MET cc_start: 0.8375 (mmp) cc_final: 0.8151 (mmt) REVERT: B 2347 MET cc_start: 0.7926 (mmp) cc_final: 0.7453 (mmp) REVERT: B 2669 LEU cc_start: 0.9061 (mt) cc_final: 0.8781 (mt) REVERT: B 2720 PHE cc_start: 0.8617 (t80) cc_final: 0.8228 (t80) REVERT: B 2840 MET cc_start: 0.8223 (mmm) cc_final: 0.7937 (mmm) REVERT: B 2843 MET cc_start: 0.7785 (ppp) cc_final: 0.7460 (ppp) REVERT: B 2867 ASN cc_start: 0.0062 (OUTLIER) cc_final: -0.1090 (m-40) REVERT: B 3104 MET cc_start: 0.8821 (ptm) cc_final: 0.8261 (ppp) REVERT: B 3296 MET cc_start: 0.9171 (pmm) cc_final: 0.8845 (pmm) REVERT: B 3318 HIS cc_start: 0.8128 (p90) cc_final: 0.7703 (p-80) REVERT: B 3978 MET cc_start: 0.8952 (ttp) cc_final: 0.8664 (ttt) REVERT: B 3985 MET cc_start: 0.8752 (mmm) cc_final: 0.8257 (mmm) REVERT: B 4019 MET cc_start: 0.8061 (mtp) cc_final: 0.7794 (mtm) REVERT: B 4048 PHE cc_start: 0.8662 (m-80) cc_final: 0.8236 (m-80) REVERT: B 4052 MET cc_start: 0.8492 (mtp) cc_final: 0.8044 (ttm) REVERT: B 4268 MET cc_start: 0.6469 (tmm) cc_final: 0.6189 (tmm) REVERT: B 4943 MET cc_start: 0.8796 (mtp) cc_final: 0.8367 (mtp) REVERT: C 81 MET cc_start: 0.8300 (tmm) cc_final: 0.7849 (tmm) REVERT: C 128 MET cc_start: 0.8662 (mtp) cc_final: 0.8416 (mtm) REVERT: C 399 MET cc_start: 0.7574 (tmm) cc_final: 0.7281 (tmm) REVERT: C 778 MET cc_start: 0.8102 (ptp) cc_final: 0.7762 (ptm) REVERT: C 956 HIS cc_start: 0.9238 (t70) cc_final: 0.8982 (t70) REVERT: C 1831 MET cc_start: 0.8834 (mtm) cc_final: 0.8611 (mtt) REVERT: C 2279 MET cc_start: 0.8615 (ptm) cc_final: 0.8412 (tmm) REVERT: C 2384 MET cc_start: 0.8502 (mpp) cc_final: 0.8202 (mpp) REVERT: C 2605 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (ppp) REVERT: C 2669 LEU cc_start: 0.9258 (mt) cc_final: 0.9013 (mm) REVERT: C 2681 MET cc_start: 0.8703 (tpt) cc_final: 0.7994 (tpt) REVERT: C 2719 TYR cc_start: 0.8616 (t80) cc_final: 0.8328 (t80) REVERT: C 2720 PHE cc_start: 0.8685 (t80) cc_final: 0.8279 (t80) REVERT: C 2724 TYR cc_start: 0.8646 (t80) cc_final: 0.8414 (t80) REVERT: C 2840 MET cc_start: 0.9014 (ptm) cc_final: 0.8314 (mmm) REVERT: C 2843 MET cc_start: 0.8000 (ppp) cc_final: 0.7467 (ppp) REVERT: C 2844 MET cc_start: 0.8661 (ppp) cc_final: 0.8427 (ppp) REVERT: C 2867 ASN cc_start: 0.0552 (OUTLIER) cc_final: -0.0804 (m-40) REVERT: C 2932 TYR cc_start: 0.8563 (t80) cc_final: 0.8083 (t80) REVERT: C 3022 PHE cc_start: 0.8398 (m-10) cc_final: 0.7988 (m-10) REVERT: C 3131 TYR cc_start: 0.8531 (m-10) cc_final: 0.8029 (m-10) REVERT: C 3241 MET cc_start: 0.8824 (mtp) cc_final: 0.8547 (ptp) REVERT: C 3318 HIS cc_start: 0.8636 (p90) cc_final: 0.8309 (p-80) REVERT: C 3322 LEU cc_start: 0.8696 (tt) cc_final: 0.8257 (mt) REVERT: C 3323 MET cc_start: 0.8494 (mmp) cc_final: 0.8160 (mmt) REVERT: C 3819 MET cc_start: 0.6177 (ptp) cc_final: 0.5946 (ptp) REVERT: C 4748 MET cc_start: 0.7168 (mpp) cc_final: 0.6694 (mpp) REVERT: C 4943 MET cc_start: 0.8783 (mtp) cc_final: 0.8313 (mtp) outliers start: 83 outliers final: 35 residues processed: 861 average time/residue: 1.2293 time to fit residues: 1888.2812 Evaluate side-chains 829 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 786 time to evaluate : 12.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 3283 ILE Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 3283 ILE Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1794 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2512 MET Chi-restraints excluded: chain C residue 2605 MET Chi-restraints excluded: chain C residue 2867 ASN Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 20.0000 chunk 1181 optimal weight: 10.0000 chunk 815 optimal weight: 30.0000 chunk 174 optimal weight: 0.0030 chunk 750 optimal weight: 30.0000 chunk 1055 optimal weight: 6.9990 chunk 1577 optimal weight: 8.9990 chunk 1670 optimal weight: 6.9990 chunk 824 optimal weight: 0.6980 chunk 1495 optimal weight: 0.0060 chunk 450 optimal weight: 5.9990 overall best weight: 2.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3304 GLN ** A3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS G 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2316 ASN ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3304 GLN B3811 GLN ** B3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3304 GLN C3811 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 141628 Z= 0.223 Angle : 0.619 16.381 191356 Z= 0.311 Chirality : 0.041 0.300 20988 Planarity : 0.005 0.136 24588 Dihedral : 5.806 71.448 19028 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 0.55 % Allowed : 6.38 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.06), residues: 17212 helix: 0.66 (0.06), residues: 8720 sheet: -0.37 (0.12), residues: 1788 loop : -0.63 (0.08), residues: 6704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D2773 HIS 0.035 0.001 HIS A2727 PHE 0.023 0.001 PHE A2975 TYR 0.038 0.001 TYR D2939 ARG 0.006 0.000 ARG E 50 *********************** 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 876 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 801 time to evaluate : 12.531 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: H 50 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.8022 (ttp-110) REVERT: A 81 MET cc_start: 0.8262 (tmm) cc_final: 0.7760 (tmm) REVERT: A 399 MET cc_start: 0.7568 (tmm) cc_final: 0.7308 (tmm) REVERT: A 403 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 678 MET cc_start: 0.7981 (ttt) cc_final: 0.7762 (ttt) REVERT: A 940 LEU cc_start: 0.9414 (mt) cc_final: 0.9188 (mt) REVERT: A 956 HIS cc_start: 0.9060 (t70) cc_final: 0.8785 (t70) REVERT: A 1165 MET cc_start: 0.8239 (mtp) cc_final: 0.7614 (mtm) REVERT: A 1487 MET cc_start: 0.8835 (mtm) cc_final: 0.8595 (mtp) REVERT: A 1494 MET cc_start: 0.7684 (tmm) cc_final: 0.7341 (tmm) REVERT: A 1694 MET cc_start: 0.8967 (tpp) cc_final: 0.8558 (tpp) REVERT: A 1906 MET cc_start: 0.8435 (mmm) cc_final: 0.8035 (mmm) REVERT: A 2066 MET cc_start: 0.8862 (mmp) cc_final: 0.8251 (mmm) REVERT: A 2142 MET cc_start: 0.8368 (tpt) cc_final: 0.8050 (tpp) REVERT: A 2347 MET cc_start: 0.7875 (mmp) cc_final: 0.7464 (mmp) REVERT: A 2493 LEU cc_start: 0.9034 (mm) cc_final: 0.8797 (mp) REVERT: A 2553 TYR cc_start: 0.7703 (t80) cc_final: 0.7119 (t80) REVERT: A 2681 MET cc_start: 0.8472 (tpt) cc_final: 0.7801 (mmm) REVERT: A 2719 TYR cc_start: 0.8596 (t80) cc_final: 0.8331 (t80) REVERT: A 2720 PHE cc_start: 0.8526 (t80) cc_final: 0.8120 (t80) REVERT: A 2724 TYR cc_start: 0.8439 (t80) cc_final: 0.8220 (t80) REVERT: A 2734 MET cc_start: 0.6857 (mmm) cc_final: 0.6514 (ptp) REVERT: A 2828 MET cc_start: 0.6847 (pmm) cc_final: 0.6179 (pmm) REVERT: A 2844 MET cc_start: 0.8498 (ppp) cc_final: 0.8243 (ppp) REVERT: A 2932 TYR cc_start: 0.8397 (t80) cc_final: 0.8040 (t80) REVERT: A 3104 MET cc_start: 0.8463 (ppp) cc_final: 0.8178 (ppp) REVERT: A 3249 TRP cc_start: 0.7797 (m100) cc_final: 0.7588 (m100) REVERT: A 3263 MET cc_start: 0.8073 (tmm) cc_final: 0.7824 (tpp) REVERT: A 3273 MET cc_start: 0.9309 (ppp) cc_final: 0.9084 (ppp) REVERT: A 3283 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 3296 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8935 (pmm) REVERT: A 3981 MET cc_start: 0.8873 (tmm) cc_final: 0.8490 (tmm) REVERT: A 4268 MET cc_start: 0.6067 (tmm) cc_final: 0.5750 (tmm) REVERT: G 58 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8212 (ptpt) REVERT: D 81 MET cc_start: 0.8402 (tmm) cc_final: 0.8057 (tmm) REVERT: D 128 MET cc_start: 0.8544 (mtp) cc_final: 0.8298 (mtp) REVERT: D 778 MET cc_start: 0.8135 (ptm) cc_final: 0.7673 (ptm) REVERT: D 956 HIS cc_start: 0.9053 (t70) cc_final: 0.8775 (t70) REVERT: D 1494 MET cc_start: 0.7716 (tmm) cc_final: 0.7488 (tmm) REVERT: D 1906 MET cc_start: 0.8478 (mmm) cc_final: 0.8074 (mmm) REVERT: D 2084 MET cc_start: 0.8828 (mtp) cc_final: 0.8566 (mtm) REVERT: D 2142 MET cc_start: 0.8473 (tpt) cc_final: 0.8198 (tpt) REVERT: D 2406 MET cc_start: 0.6784 (tmm) cc_final: 0.6404 (tmm) REVERT: D 2534 LEU cc_start: 0.9058 (mt) cc_final: 0.8668 (tp) REVERT: D 2540 HIS cc_start: 0.7521 (p-80) cc_final: 0.7280 (p-80) REVERT: D 2681 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: D 2688 MET cc_start: 0.1095 (ptt) cc_final: 0.0733 (ptt) REVERT: D 2719 TYR cc_start: 0.8693 (t80) cc_final: 0.8381 (t80) REVERT: D 2720 PHE cc_start: 0.8575 (t80) cc_final: 0.8146 (t80) REVERT: D 2724 TYR cc_start: 0.8739 (t80) cc_final: 0.8406 (t80) REVERT: D 2771 TYR cc_start: 0.8466 (m-80) cc_final: 0.7856 (m-10) REVERT: D 2782 MET cc_start: 0.8102 (ppp) cc_final: 0.7901 (ppp) REVERT: D 2783 LEU cc_start: 0.9342 (mt) cc_final: 0.8935 (mt) REVERT: D 2932 TYR cc_start: 0.8617 (t80) cc_final: 0.8269 (t80) REVERT: D 3072 MET cc_start: 0.8867 (mmm) cc_final: 0.8320 (mmm) REVERT: D 3134 LEU cc_start: 0.9222 (mt) cc_final: 0.8933 (mt) REVERT: D 3184 TYR cc_start: 0.8556 (m-10) cc_final: 0.8334 (m-10) REVERT: D 3819 MET cc_start: 0.6736 (ptp) cc_final: 0.6462 (ptp) REVERT: D 4292 MET cc_start: 0.8208 (mmm) cc_final: 0.7898 (mmm) REVERT: D 4504 MET cc_start: 0.7634 (mmm) cc_final: 0.7423 (mmp) REVERT: B 81 MET cc_start: 0.8104 (tmm) cc_final: 0.7749 (tmm) REVERT: B 399 MET cc_start: 0.7559 (tmm) cc_final: 0.7203 (tmm) REVERT: B 403 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 678 MET cc_start: 0.7623 (ttm) cc_final: 0.7297 (ttt) REVERT: B 940 LEU cc_start: 0.9366 (mt) cc_final: 0.9103 (mt) REVERT: B 956 HIS cc_start: 0.9138 (t70) cc_final: 0.8878 (t70) REVERT: B 1035 TYR cc_start: 0.7417 (t80) cc_final: 0.6927 (t80) REVERT: B 1113 MET cc_start: 0.8058 (mtm) cc_final: 0.7751 (mtp) REVERT: B 1165 MET cc_start: 0.8081 (mtp) cc_final: 0.7716 (mtp) REVERT: B 1168 MET cc_start: 0.8614 (mmm) cc_final: 0.8272 (mmm) REVERT: B 1215 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7997 (mtt) REVERT: B 1249 MET cc_start: 0.7907 (tpp) cc_final: 0.7679 (tpt) REVERT: B 1906 MET cc_start: 0.8284 (mmm) cc_final: 0.7989 (mmm) REVERT: B 1975 MET cc_start: 0.8977 (ptt) cc_final: 0.8763 (ppp) REVERT: B 2234 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: B 2279 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8371 (ptp) REVERT: B 2347 MET cc_start: 0.7983 (mmp) cc_final: 0.7481 (mmp) REVERT: B 2384 MET cc_start: 0.8478 (mpp) cc_final: 0.8190 (mpp) REVERT: B 2585 MET cc_start: 0.7877 (mpp) cc_final: 0.7645 (pmm) REVERT: B 2669 LEU cc_start: 0.9064 (mt) cc_final: 0.8769 (mt) REVERT: B 2720 PHE cc_start: 0.8622 (t80) cc_final: 0.8234 (t80) REVERT: B 2843 MET cc_start: 0.7789 (ppp) cc_final: 0.7421 (ppp) REVERT: B 2844 MET cc_start: 0.8621 (ppp) cc_final: 0.8336 (ppp) REVERT: B 3072 MET cc_start: 0.8584 (mmm) cc_final: 0.8268 (mmm) REVERT: B 3159 LEU cc_start: 0.9262 (mm) cc_final: 0.8586 (pp) REVERT: B 3241 MET cc_start: 0.8901 (mtp) cc_final: 0.8667 (mtp) REVERT: B 3318 HIS cc_start: 0.7813 (p90) cc_final: 0.7469 (p-80) REVERT: B 3319 PHE cc_start: 0.8035 (m-10) cc_final: 0.7647 (m-80) REVERT: B 3739 MET cc_start: 0.8819 (ttp) cc_final: 0.8572 (ttp) REVERT: B 3819 MET cc_start: 0.6659 (pmm) cc_final: 0.5689 (pmm) REVERT: B 3978 MET cc_start: 0.8944 (ttp) cc_final: 0.8667 (ttt) REVERT: B 4052 MET cc_start: 0.8459 (mtp) cc_final: 0.8088 (ttm) REVERT: B 4268 MET cc_start: 0.6515 (tmm) cc_final: 0.6242 (tmm) REVERT: B 4748 MET cc_start: 0.7338 (mpp) cc_final: 0.7118 (mpp) REVERT: B 4943 MET cc_start: 0.8789 (mtp) cc_final: 0.8364 (mtp) REVERT: C 81 MET cc_start: 0.8310 (tmm) cc_final: 0.7855 (tmm) REVERT: C 128 MET cc_start: 0.8682 (mtp) cc_final: 0.8432 (mtm) REVERT: C 349 MET cc_start: 0.8505 (mmm) cc_final: 0.8229 (mmt) REVERT: C 399 MET cc_start: 0.7576 (tmm) cc_final: 0.7277 (tmm) REVERT: C 956 HIS cc_start: 0.9236 (t70) cc_final: 0.8969 (t70) REVERT: C 995 MET cc_start: 0.8534 (mpp) cc_final: 0.8302 (mpp) REVERT: C 1165 MET cc_start: 0.8211 (mtp) cc_final: 0.7887 (mtp) REVERT: C 1694 MET cc_start: 0.8927 (tpp) cc_final: 0.8636 (tpp) REVERT: C 1831 MET cc_start: 0.8844 (mtm) cc_final: 0.8599 (mtt) REVERT: C 2066 MET cc_start: 0.8825 (mmt) cc_final: 0.8526 (mmp) REVERT: C 2384 MET cc_start: 0.8426 (mpp) cc_final: 0.8156 (mpp) REVERT: C 2585 MET cc_start: 0.7897 (pmm) cc_final: 0.6850 (pmm) REVERT: C 2615 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: C 2669 LEU cc_start: 0.9250 (mt) cc_final: 0.9007 (mm) REVERT: C 2681 MET cc_start: 0.8638 (tpt) cc_final: 0.7843 (tpt) REVERT: C 2719 TYR cc_start: 0.8609 (t80) cc_final: 0.8321 (t80) REVERT: C 2720 PHE cc_start: 0.8690 (t80) cc_final: 0.8294 (t80) REVERT: C 2724 TYR cc_start: 0.8618 (t80) cc_final: 0.8402 (t80) REVERT: C 2840 MET cc_start: 0.8999 (ptm) cc_final: 0.8280 (mmm) REVERT: C 2843 MET cc_start: 0.8045 (ppp) cc_final: 0.7494 (ppp) REVERT: C 2844 MET cc_start: 0.8748 (ppp) cc_final: 0.8492 (ppp) REVERT: C 2932 TYR cc_start: 0.8569 (t80) cc_final: 0.8083 (t80) REVERT: C 3022 PHE cc_start: 0.8430 (m-10) cc_final: 0.7975 (m-10) REVERT: C 3263 MET cc_start: 0.8263 (tmm) cc_final: 0.8004 (tpt) REVERT: C 3322 LEU cc_start: 0.8645 (tt) cc_final: 0.8170 (mt) REVERT: C 3323 MET cc_start: 0.8475 (mmp) cc_final: 0.8162 (mmt) REVERT: C 3819 MET cc_start: 0.6196 (ptp) cc_final: 0.5938 (ptp) REVERT: C 4002 MET cc_start: 0.8503 (tmm) cc_final: 0.8213 (tmm) REVERT: C 4279 MET cc_start: 0.7263 (mmm) cc_final: 0.7020 (mtm) REVERT: C 4707 MET cc_start: 0.8040 (ttt) cc_final: 0.7817 (ttm) REVERT: C 4748 MET cc_start: 0.7169 (mpp) cc_final: 0.6680 (mpp) REVERT: C 4943 MET cc_start: 0.8778 (mtp) cc_final: 0.8328 (mtp) outliers start: 75 outliers final: 42 residues processed: 837 average time/residue: 1.1650 time to fit residues: 1728.2134 Evaluate side-chains 836 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 785 time to evaluate : 12.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1794 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3283 ILE Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 1729 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 1794 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2615 GLU Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2512 MET Chi-restraints excluded: chain C residue 2615 GLU Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 6.9990 chunk 948 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 1243 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 1425 optimal weight: 2.9990 chunk 1154 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 852 optimal weight: 4.9990 chunk 1499 optimal weight: 10.0000 chunk 421 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3286 ASN ** A3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3665 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS C1562 ASN ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 141628 Z= 0.271 Angle : 0.617 19.380 191356 Z= 0.311 Chirality : 0.042 0.303 20988 Planarity : 0.005 0.133 24588 Dihedral : 5.623 72.163 19028 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 0.57 % Allowed : 7.05 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.07), residues: 17212 helix: 0.92 (0.06), residues: 8700 sheet: -0.31 (0.13), residues: 1740 loop : -0.58 (0.08), residues: 6772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 893 HIS 0.020 0.001 HIS F 26 PHE 0.025 0.002 PHE D2963 TYR 0.033 0.002 TYR D2939 ARG 0.007 0.000 ARG F 50 *********************** 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 875 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 796 time to evaluate : 12.055 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: H 4 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6858 (tm-30) REVERT: A 81 MET cc_start: 0.8279 (tmm) cc_final: 0.7779 (tmm) REVERT: A 399 MET cc_start: 0.7584 (tmm) cc_final: 0.7320 (tmm) REVERT: A 403 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 940 LEU cc_start: 0.9409 (mt) cc_final: 0.9186 (mt) REVERT: A 956 HIS cc_start: 0.9044 (t70) cc_final: 0.8761 (t70) REVERT: A 1165 MET cc_start: 0.8261 (mtp) cc_final: 0.7948 (mtp) REVERT: A 1487 MET cc_start: 0.8839 (mtm) cc_final: 0.8618 (mtp) REVERT: A 1494 MET cc_start: 0.7745 (tmm) cc_final: 0.7435 (tmm) REVERT: A 1694 MET cc_start: 0.8961 (tpp) cc_final: 0.8574 (tpp) REVERT: A 2066 MET cc_start: 0.8813 (mmp) cc_final: 0.8237 (mmm) REVERT: A 2142 MET cc_start: 0.8353 (tpt) cc_final: 0.8013 (tpp) REVERT: A 2347 MET cc_start: 0.7954 (mmp) cc_final: 0.7529 (mmp) REVERT: A 2493 LEU cc_start: 0.9050 (mm) cc_final: 0.8815 (mp) REVERT: A 2553 TYR cc_start: 0.7743 (t80) cc_final: 0.7130 (t80) REVERT: A 2681 MET cc_start: 0.8490 (tpt) cc_final: 0.7513 (tpp) REVERT: A 2695 MET cc_start: 0.6344 (pmm) cc_final: 0.6091 (pmm) REVERT: A 2719 TYR cc_start: 0.8598 (t80) cc_final: 0.8183 (t80) REVERT: A 2720 PHE cc_start: 0.8556 (t80) cc_final: 0.8127 (t80) REVERT: A 2724 TYR cc_start: 0.8449 (t80) cc_final: 0.8236 (t80) REVERT: A 2734 MET cc_start: 0.6927 (mmm) cc_final: 0.6671 (ptp) REVERT: A 2828 MET cc_start: 0.6984 (pmm) cc_final: 0.6312 (pmm) REVERT: A 2932 TYR cc_start: 0.8416 (t80) cc_final: 0.8041 (t80) REVERT: A 3022 PHE cc_start: 0.8284 (m-10) cc_final: 0.7865 (m-10) REVERT: A 3104 MET cc_start: 0.8500 (ppp) cc_final: 0.8197 (ppp) REVERT: A 3283 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 3296 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8971 (pmm) REVERT: A 3981 MET cc_start: 0.8904 (tmm) cc_final: 0.8503 (tmm) REVERT: A 4019 MET cc_start: 0.8396 (ttp) cc_final: 0.8005 (ttt) REVERT: A 4268 MET cc_start: 0.6105 (tmm) cc_final: 0.5828 (tmm) REVERT: F 18 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8508 (mtmm) REVERT: G 50 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7997 (ttp-110) REVERT: D 81 MET cc_start: 0.8402 (tmm) cc_final: 0.8019 (tmm) REVERT: D 128 MET cc_start: 0.8580 (mtp) cc_final: 0.8359 (mtp) REVERT: D 778 MET cc_start: 0.8186 (ptm) cc_final: 0.7971 (ptp) REVERT: D 956 HIS cc_start: 0.9052 (t70) cc_final: 0.8772 (t70) REVERT: D 1165 MET cc_start: 0.8199 (mtp) cc_final: 0.7791 (mtp) REVERT: D 1215 MET cc_start: 0.8301 (mtt) cc_final: 0.8036 (mtt) REVERT: D 1494 MET cc_start: 0.7768 (tmm) cc_final: 0.7537 (tmm) REVERT: D 2084 MET cc_start: 0.8871 (mtp) cc_final: 0.8600 (mtm) REVERT: D 2142 MET cc_start: 0.8460 (tpt) cc_final: 0.8209 (tpt) REVERT: D 2389 MET cc_start: 0.7810 (ptt) cc_final: 0.7474 (ptt) REVERT: D 2534 LEU cc_start: 0.9066 (mt) cc_final: 0.8670 (tp) REVERT: D 2540 HIS cc_start: 0.7550 (p-80) cc_final: 0.7290 (p-80) REVERT: D 2681 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7800 (mmm) REVERT: D 2688 MET cc_start: 0.1094 (ptt) cc_final: 0.0725 (ptt) REVERT: D 2719 TYR cc_start: 0.8681 (t80) cc_final: 0.8376 (t80) REVERT: D 2720 PHE cc_start: 0.8619 (t80) cc_final: 0.8187 (t80) REVERT: D 2724 TYR cc_start: 0.8699 (t80) cc_final: 0.8346 (t80) REVERT: D 2771 TYR cc_start: 0.8503 (m-80) cc_final: 0.7942 (m-10) REVERT: D 2932 TYR cc_start: 0.8622 (t80) cc_final: 0.8268 (t80) REVERT: D 3072 MET cc_start: 0.8936 (mmm) cc_final: 0.8392 (mmm) REVERT: D 3134 LEU cc_start: 0.9247 (mt) cc_final: 0.8966 (mt) REVERT: D 3819 MET cc_start: 0.6748 (ptp) cc_final: 0.6464 (ptp) REVERT: B 81 MET cc_start: 0.8134 (tmm) cc_final: 0.7793 (tmm) REVERT: B 399 MET cc_start: 0.7585 (tmm) cc_final: 0.7207 (tmm) REVERT: B 940 LEU cc_start: 0.9362 (mt) cc_final: 0.9097 (mt) REVERT: B 956 HIS cc_start: 0.9125 (t70) cc_final: 0.8865 (t70) REVERT: B 1035 TYR cc_start: 0.7469 (t80) cc_final: 0.6990 (t80) REVERT: B 1113 MET cc_start: 0.8102 (mtm) cc_final: 0.7807 (mtp) REVERT: B 1165 MET cc_start: 0.8140 (mtp) cc_final: 0.7751 (mtp) REVERT: B 1168 MET cc_start: 0.8622 (mmm) cc_final: 0.8233 (mmm) REVERT: B 1215 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: B 1906 MET cc_start: 0.8363 (mmm) cc_final: 0.8055 (mmm) REVERT: B 2066 MET cc_start: 0.8774 (mmp) cc_final: 0.8425 (mmm) REVERT: B 2234 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: B 2279 MET cc_start: 0.8626 (ptt) cc_final: 0.8406 (ptp) REVERT: B 2347 MET cc_start: 0.8050 (mmp) cc_final: 0.7526 (mmp) REVERT: B 2384 MET cc_start: 0.8502 (mpp) cc_final: 0.8233 (mpp) REVERT: B 2493 LEU cc_start: 0.9024 (mm) cc_final: 0.8810 (mp) REVERT: B 2669 LEU cc_start: 0.9098 (mt) cc_final: 0.8831 (tp) REVERT: B 2720 PHE cc_start: 0.8640 (t80) cc_final: 0.8254 (t80) REVERT: B 2843 MET cc_start: 0.7803 (ppp) cc_final: 0.7351 (ppp) REVERT: B 2844 MET cc_start: 0.8706 (ppp) cc_final: 0.8389 (ppp) REVERT: B 2932 TYR cc_start: 0.8322 (t80) cc_final: 0.7971 (t80) REVERT: B 3159 LEU cc_start: 0.9288 (mm) cc_final: 0.8740 (pp) REVERT: B 3241 MET cc_start: 0.8934 (mtp) cc_final: 0.8722 (mtp) REVERT: B 3246 MET cc_start: 0.8641 (tmm) cc_final: 0.8383 (tmm) REVERT: B 3739 MET cc_start: 0.8826 (ttp) cc_final: 0.8581 (ttp) REVERT: B 3819 MET cc_start: 0.6836 (pmm) cc_final: 0.5797 (pmm) REVERT: B 3978 MET cc_start: 0.8988 (ttp) cc_final: 0.8736 (ttt) REVERT: B 4048 PHE cc_start: 0.8650 (m-80) cc_final: 0.8440 (m-80) REVERT: B 4052 MET cc_start: 0.8514 (mtp) cc_final: 0.8081 (ttm) REVERT: B 4256 MET cc_start: 0.8249 (mmt) cc_final: 0.8003 (mmt) REVERT: B 4268 MET cc_start: 0.6464 (tmm) cc_final: 0.6190 (tmm) REVERT: B 4292 MET cc_start: 0.8158 (mmm) cc_final: 0.7861 (mmm) REVERT: B 4943 MET cc_start: 0.8804 (mtp) cc_final: 0.8388 (mtp) REVERT: C 81 MET cc_start: 0.8322 (tmm) cc_final: 0.7885 (tmm) REVERT: C 349 MET cc_start: 0.8507 (mmm) cc_final: 0.8234 (mmt) REVERT: C 399 MET cc_start: 0.7560 (tmm) cc_final: 0.7254 (tmm) REVERT: C 956 HIS cc_start: 0.9252 (t70) cc_final: 0.8989 (t70) REVERT: C 995 MET cc_start: 0.8554 (mpp) cc_final: 0.8311 (mpp) REVERT: C 1694 MET cc_start: 0.8963 (tpp) cc_final: 0.8636 (tpp) REVERT: C 1831 MET cc_start: 0.8856 (mtm) cc_final: 0.8601 (mtt) REVERT: C 2384 MET cc_start: 0.8475 (mpp) cc_final: 0.8156 (mpp) REVERT: C 2669 LEU cc_start: 0.9264 (mt) cc_final: 0.9027 (mm) REVERT: C 2681 MET cc_start: 0.8596 (tpt) cc_final: 0.7800 (tpt) REVERT: C 2719 TYR cc_start: 0.8623 (t80) cc_final: 0.8325 (t80) REVERT: C 2720 PHE cc_start: 0.8697 (t80) cc_final: 0.8300 (t80) REVERT: C 2840 MET cc_start: 0.9008 (ptm) cc_final: 0.8286 (mmm) REVERT: C 2843 MET cc_start: 0.8075 (ppp) cc_final: 0.7588 (ppp) REVERT: C 2844 MET cc_start: 0.8783 (ppp) cc_final: 0.8539 (ppp) REVERT: C 2932 TYR cc_start: 0.8571 (t80) cc_final: 0.8070 (t80) REVERT: C 2944 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: C 2963 PHE cc_start: 0.8470 (t80) cc_final: 0.8266 (t80) REVERT: C 3022 PHE cc_start: 0.8439 (m-10) cc_final: 0.7978 (m-10) REVERT: C 3263 MET cc_start: 0.8201 (tmm) cc_final: 0.7969 (tpt) REVERT: C 3322 LEU cc_start: 0.8672 (tt) cc_final: 0.8175 (mt) REVERT: C 3323 MET cc_start: 0.8529 (mmp) cc_final: 0.8201 (mmt) REVERT: C 3981 MET cc_start: 0.8887 (tmm) cc_final: 0.8445 (ttm) REVERT: C 4279 MET cc_start: 0.7240 (mmm) cc_final: 0.6993 (mtm) REVERT: C 4306 PHE cc_start: 0.6686 (m-10) cc_final: 0.6477 (t80) REVERT: C 4707 MET cc_start: 0.8063 (ttt) cc_final: 0.7832 (ttm) REVERT: C 4748 MET cc_start: 0.7150 (mpp) cc_final: 0.6618 (mpp) REVERT: C 4943 MET cc_start: 0.8766 (mtp) cc_final: 0.8334 (mtp) outliers start: 79 outliers final: 42 residues processed: 836 average time/residue: 1.1982 time to fit residues: 1778.3361 Evaluate side-chains 827 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 778 time to evaluate : 12.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3283 ILE Chi-restraints excluded: chain A residue 3296 MET Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2615 GLU Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 10.0000 chunk 1504 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 980 optimal weight: 30.0000 chunk 412 optimal weight: 3.9990 chunk 1671 optimal weight: 5.9990 chunk 1387 optimal weight: 7.9990 chunk 774 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 553 optimal weight: 7.9990 chunk 877 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 HIS E 26 HIS F 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2410 HIS D2727 HIS ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4088 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3286 ASN ** C3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 141628 Z= 0.305 Angle : 0.629 16.859 191356 Z= 0.316 Chirality : 0.042 0.472 20988 Planarity : 0.005 0.132 24588 Dihedral : 5.511 73.124 19028 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 0.59 % Allowed : 7.34 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.07), residues: 17212 helix: 1.11 (0.06), residues: 8680 sheet: -0.29 (0.12), residues: 1744 loop : -0.54 (0.08), residues: 6788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 893 HIS 0.018 0.001 HIS B2410 PHE 0.023 0.002 PHE C3162 TYR 0.029 0.002 TYR D2939 ARG 0.015 0.000 ARG B 801 *********************** 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 883 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 802 time to evaluate : 12.282 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: H 4 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 81 MET cc_start: 0.8291 (tmm) cc_final: 0.7800 (tmm) REVERT: A 399 MET cc_start: 0.7587 (tmm) cc_final: 0.7319 (tmm) REVERT: A 403 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 940 LEU cc_start: 0.9407 (mt) cc_final: 0.9171 (mt) REVERT: A 956 HIS cc_start: 0.9027 (t70) cc_final: 0.8746 (t70) REVERT: A 1487 MET cc_start: 0.8830 (mtm) cc_final: 0.8620 (mtp) REVERT: A 1494 MET cc_start: 0.7747 (tmm) cc_final: 0.7453 (tmm) REVERT: A 1694 MET cc_start: 0.8965 (tpp) cc_final: 0.8595 (tpp) REVERT: A 1948 MET cc_start: 0.7868 (mmp) cc_final: 0.7640 (mmm) REVERT: A 2142 MET cc_start: 0.8353 (tpt) cc_final: 0.8011 (tpp) REVERT: A 2347 MET cc_start: 0.8025 (mmp) cc_final: 0.7612 (mmp) REVERT: A 2493 LEU cc_start: 0.9071 (mm) cc_final: 0.8840 (mp) REVERT: A 2534 LEU cc_start: 0.9187 (mt) cc_final: 0.8805 (tp) REVERT: A 2553 TYR cc_start: 0.7790 (t80) cc_final: 0.7231 (t80) REVERT: A 2681 MET cc_start: 0.8509 (tpt) cc_final: 0.7556 (tpp) REVERT: A 2695 MET cc_start: 0.6429 (pmm) cc_final: 0.6152 (pmm) REVERT: A 2719 TYR cc_start: 0.8580 (t80) cc_final: 0.8159 (t80) REVERT: A 2720 PHE cc_start: 0.8569 (t80) cc_final: 0.8144 (t80) REVERT: A 2724 TYR cc_start: 0.8373 (t80) cc_final: 0.8112 (t80) REVERT: A 2734 MET cc_start: 0.6977 (mmm) cc_final: 0.6742 (ptp) REVERT: A 2844 MET cc_start: 0.8428 (ppp) cc_final: 0.8171 (ppp) REVERT: A 2932 TYR cc_start: 0.8443 (t80) cc_final: 0.8053 (t80) REVERT: A 3022 PHE cc_start: 0.8300 (m-10) cc_final: 0.8015 (m-10) REVERT: A 3072 MET cc_start: 0.9002 (mmp) cc_final: 0.8209 (mmm) REVERT: A 3104 MET cc_start: 0.8520 (ppp) cc_final: 0.8204 (ppp) REVERT: A 3159 LEU cc_start: 0.9322 (mm) cc_final: 0.8717 (pp) REVERT: A 3981 MET cc_start: 0.8918 (tmm) cc_final: 0.8493 (tmm) REVERT: A 4268 MET cc_start: 0.6161 (tmm) cc_final: 0.5872 (tmm) REVERT: F 18 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8477 (mtmm) REVERT: G 18 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8450 (mtmm) REVERT: D 81 MET cc_start: 0.8390 (tmm) cc_final: 0.7962 (tmm) REVERT: D 128 MET cc_start: 0.8582 (mtp) cc_final: 0.8367 (mtp) REVERT: D 778 MET cc_start: 0.8243 (ptm) cc_final: 0.7815 (ptm) REVERT: D 956 HIS cc_start: 0.9044 (t70) cc_final: 0.8767 (t70) REVERT: D 1165 MET cc_start: 0.8236 (mtp) cc_final: 0.7846 (mtp) REVERT: D 1215 MET cc_start: 0.8332 (mtt) cc_final: 0.8068 (mtt) REVERT: D 1494 MET cc_start: 0.7785 (tmm) cc_final: 0.7568 (tmm) REVERT: D 1948 MET cc_start: 0.7967 (mmp) cc_final: 0.7733 (mmm) REVERT: D 2084 MET cc_start: 0.8899 (mtp) cc_final: 0.8621 (mtm) REVERT: D 2142 MET cc_start: 0.8458 (tpt) cc_final: 0.8198 (tpt) REVERT: D 2389 MET cc_start: 0.7840 (ptt) cc_final: 0.7537 (ptt) REVERT: D 2534 LEU cc_start: 0.9077 (mt) cc_final: 0.8675 (tp) REVERT: D 2681 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: D 2688 MET cc_start: 0.1011 (ptt) cc_final: 0.0727 (ptt) REVERT: D 2719 TYR cc_start: 0.8679 (t80) cc_final: 0.8279 (t80) REVERT: D 2720 PHE cc_start: 0.8603 (t80) cc_final: 0.8118 (t80) REVERT: D 2724 TYR cc_start: 0.8712 (t80) cc_final: 0.8404 (t80) REVERT: D 2771 TYR cc_start: 0.8482 (m-80) cc_final: 0.7892 (m-10) REVERT: D 2932 TYR cc_start: 0.8628 (t80) cc_final: 0.8261 (t80) REVERT: D 3072 MET cc_start: 0.8926 (mmm) cc_final: 0.8360 (mmm) REVERT: D 3104 MET cc_start: 0.8505 (ppp) cc_final: 0.8119 (ppp) REVERT: D 3134 LEU cc_start: 0.9260 (mt) cc_final: 0.8995 (mt) REVERT: D 3246 MET cc_start: 0.8708 (tmm) cc_final: 0.8457 (tmm) REVERT: D 3273 MET cc_start: 0.9264 (ppp) cc_final: 0.8890 (ppp) REVERT: D 3819 MET cc_start: 0.6762 (ptp) cc_final: 0.6468 (ptp) REVERT: B 81 MET cc_start: 0.8172 (tmm) cc_final: 0.7756 (tmm) REVERT: B 399 MET cc_start: 0.7589 (tmm) cc_final: 0.7212 (tmm) REVERT: B 940 LEU cc_start: 0.9367 (mt) cc_final: 0.9103 (mt) REVERT: B 956 HIS cc_start: 0.9109 (t70) cc_final: 0.8847 (t70) REVERT: B 1165 MET cc_start: 0.8181 (mtp) cc_final: 0.7797 (mtp) REVERT: B 1168 MET cc_start: 0.8619 (mmm) cc_final: 0.8200 (mmm) REVERT: B 1215 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: B 1906 MET cc_start: 0.8416 (mmm) cc_final: 0.8106 (mmm) REVERT: B 2066 MET cc_start: 0.8769 (mmp) cc_final: 0.8363 (mmm) REVERT: B 2234 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: B 2279 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (ptp) REVERT: B 2347 MET cc_start: 0.8120 (mmp) cc_final: 0.7614 (mmp) REVERT: B 2384 MET cc_start: 0.8537 (mpp) cc_final: 0.8267 (mpp) REVERT: B 2493 LEU cc_start: 0.9049 (mm) cc_final: 0.8840 (mp) REVERT: B 2585 MET cc_start: 0.7644 (pmm) cc_final: 0.7193 (pmm) REVERT: B 2652 LEU cc_start: 0.9022 (mp) cc_final: 0.8810 (mm) REVERT: B 2719 TYR cc_start: 0.8559 (t80) cc_final: 0.8287 (t80) REVERT: B 2720 PHE cc_start: 0.8650 (t80) cc_final: 0.8286 (t80) REVERT: B 2840 MET cc_start: 0.8123 (mmm) cc_final: 0.7628 (mmm) REVERT: B 2843 MET cc_start: 0.7839 (ppp) cc_final: 0.7332 (ppp) REVERT: B 2844 MET cc_start: 0.8737 (ppp) cc_final: 0.8413 (ppp) REVERT: B 2932 TYR cc_start: 0.8342 (t80) cc_final: 0.7982 (t80) REVERT: B 3072 MET cc_start: 0.8631 (mmm) cc_final: 0.8428 (mmm) REVERT: B 3109 PHE cc_start: 0.8762 (m-10) cc_final: 0.8503 (m-10) REVERT: B 3241 MET cc_start: 0.8946 (mtp) cc_final: 0.8695 (mtp) REVERT: B 3246 MET cc_start: 0.8646 (tmm) cc_final: 0.8405 (tmm) REVERT: B 3819 MET cc_start: 0.6942 (pmm) cc_final: 0.6098 (pmm) REVERT: B 3978 MET cc_start: 0.9005 (ttp) cc_final: 0.8760 (ttt) REVERT: B 4048 PHE cc_start: 0.8679 (m-80) cc_final: 0.8389 (m-80) REVERT: B 4052 MET cc_start: 0.8543 (mtp) cc_final: 0.8080 (ttm) REVERT: B 4256 MET cc_start: 0.8240 (mmt) cc_final: 0.8035 (mmt) REVERT: B 4268 MET cc_start: 0.6451 (tmm) cc_final: 0.6144 (tmm) REVERT: B 4748 MET cc_start: 0.7258 (mpp) cc_final: 0.6995 (mpp) REVERT: B 4943 MET cc_start: 0.8820 (mtp) cc_final: 0.8412 (mtp) REVERT: C 81 MET cc_start: 0.8323 (tmm) cc_final: 0.7906 (tmm) REVERT: C 128 MET cc_start: 0.8681 (mtp) cc_final: 0.8409 (mtp) REVERT: C 349 MET cc_start: 0.8488 (mmm) cc_final: 0.8208 (mmt) REVERT: C 399 MET cc_start: 0.7570 (tmm) cc_final: 0.7267 (tmm) REVERT: C 956 HIS cc_start: 0.9253 (t70) cc_final: 0.8993 (t70) REVERT: C 1165 MET cc_start: 0.8191 (mtp) cc_final: 0.7667 (mtp) REVERT: C 1249 MET cc_start: 0.7946 (tpp) cc_final: 0.7723 (tpt) REVERT: C 1494 MET cc_start: 0.7496 (tmm) cc_final: 0.7186 (tmm) REVERT: C 1694 MET cc_start: 0.8987 (tpp) cc_final: 0.8591 (tpp) REVERT: C 2066 MET cc_start: 0.8811 (mmt) cc_final: 0.8475 (mmm) REVERT: C 2279 MET cc_start: 0.8705 (ptt) cc_final: 0.8327 (tmm) REVERT: C 2384 MET cc_start: 0.8531 (mpp) cc_final: 0.8176 (mpp) REVERT: C 2669 LEU cc_start: 0.9269 (mt) cc_final: 0.9033 (tp) REVERT: C 2681 MET cc_start: 0.8589 (tpt) cc_final: 0.7818 (tpt) REVERT: C 2719 TYR cc_start: 0.8634 (t80) cc_final: 0.8323 (t80) REVERT: C 2720 PHE cc_start: 0.8715 (t80) cc_final: 0.8310 (t80) REVERT: C 2840 MET cc_start: 0.9012 (ptm) cc_final: 0.8252 (mmt) REVERT: C 2843 MET cc_start: 0.8122 (ppp) cc_final: 0.7568 (ppp) REVERT: C 2844 MET cc_start: 0.8774 (ppp) cc_final: 0.8513 (ppp) REVERT: C 2932 TYR cc_start: 0.8571 (t80) cc_final: 0.8126 (t80) REVERT: C 2944 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: C 3022 PHE cc_start: 0.8446 (m-10) cc_final: 0.8012 (m-10) REVERT: C 3263 MET cc_start: 0.8155 (tmm) cc_final: 0.7927 (tpt) REVERT: C 3322 LEU cc_start: 0.8669 (tt) cc_final: 0.8180 (mt) REVERT: C 3323 MET cc_start: 0.8572 (mmp) cc_final: 0.8255 (mmt) REVERT: C 3981 MET cc_start: 0.8890 (tmm) cc_final: 0.8420 (ttm) REVERT: C 4279 MET cc_start: 0.7266 (mmm) cc_final: 0.7052 (mtm) REVERT: C 4306 PHE cc_start: 0.6711 (m-10) cc_final: 0.6486 (t80) REVERT: C 4748 MET cc_start: 0.7139 (mpp) cc_final: 0.6575 (mpp) REVERT: C 4943 MET cc_start: 0.8767 (mtp) cc_final: 0.8334 (mtp) outliers start: 81 outliers final: 56 residues processed: 849 average time/residue: 1.1655 time to fit residues: 1757.0703 Evaluate side-chains 847 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 785 time to evaluate : 12.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1794 MET Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3821 THR Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 3075 LEU Chi-restraints excluded: chain D residue 3318 HIS Chi-restraints excluded: chain D residue 3821 THR Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2615 GLU Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 3318 HIS Chi-restraints excluded: chain C residue 3821 THR Chi-restraints excluded: chain C residue 4258 MET 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: 40.0000 chunk 952 optimal weight: 8.9990 chunk 1220 optimal weight: 4.9990 chunk 945 optimal weight: 5.9990 chunk 1407 optimal weight: 6.9990 chunk 933 optimal weight: 4.9990 chunk 1665 optimal weight: 9.9990 chunk 1042 optimal weight: 10.0000 chunk 1015 optimal weight: 9.9990 chunk 768 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: H 26 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 ASN ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3665 HIS E 26 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1631 HIS D1836 ASN ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3286 ASN D3304 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 HIS ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3286 ASN B3318 HIS ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4075 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1631 HIS ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 141628 Z= 0.349 Angle : 0.642 17.017 191356 Z= 0.323 Chirality : 0.043 0.473 20988 Planarity : 0.005 0.131 24588 Dihedral : 5.494 74.995 19028 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.65 % Allowed : 7.59 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.07), residues: 17212 helix: 1.21 (0.06), residues: 8692 sheet: -0.34 (0.13), residues: 1696 loop : -0.54 (0.08), residues: 6824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 893 HIS 0.026 0.001 HIS E 26 PHE 0.026 0.002 PHE D2963 TYR 0.030 0.002 TYR B2939 ARG 0.007 0.001 ARG F 50 *********************** 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 892 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 801 time to evaluate : 15.010 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: H 4 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6818 (tm-30) REVERT: A 81 MET cc_start: 0.8304 (tmm) cc_final: 0.7808 (tmm) REVERT: A 399 MET cc_start: 0.7628 (tmm) cc_final: 0.7354 (tmm) REVERT: A 403 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 892 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9314 (mt) REVERT: A 940 LEU cc_start: 0.9414 (mt) cc_final: 0.9180 (mt) REVERT: A 956 HIS cc_start: 0.9010 (t70) cc_final: 0.8727 (t70) REVERT: A 1494 MET cc_start: 0.7789 (tmm) cc_final: 0.7509 (tmm) REVERT: A 1948 MET cc_start: 0.7941 (mmp) cc_final: 0.7698 (mmm) REVERT: A 2142 MET cc_start: 0.8376 (tpt) cc_final: 0.8029 (tpp) REVERT: A 2347 MET cc_start: 0.8136 (mmp) cc_final: 0.7711 (mmp) REVERT: A 2493 LEU cc_start: 0.9057 (mm) cc_final: 0.8840 (mp) REVERT: A 2534 LEU cc_start: 0.9212 (mt) cc_final: 0.8836 (tp) REVERT: A 2553 TYR cc_start: 0.7871 (t80) cc_final: 0.7313 (t80) REVERT: A 2681 MET cc_start: 0.8572 (tpt) cc_final: 0.7661 (tpp) REVERT: A 2695 MET cc_start: 0.6613 (pmm) cc_final: 0.6328 (pmm) REVERT: A 2719 TYR cc_start: 0.8587 (t80) cc_final: 0.8156 (t80) REVERT: A 2720 PHE cc_start: 0.8572 (t80) cc_final: 0.8141 (t80) REVERT: A 2724 TYR cc_start: 0.8340 (t80) cc_final: 0.8123 (t80) REVERT: A 2844 MET cc_start: 0.8586 (ppp) cc_final: 0.8294 (ppp) REVERT: A 2932 TYR cc_start: 0.8456 (t80) cc_final: 0.8052 (t80) REVERT: A 3022 PHE cc_start: 0.8324 (m-10) cc_final: 0.8039 (m-10) REVERT: A 3072 MET cc_start: 0.8982 (mmp) cc_final: 0.8178 (mmm) REVERT: A 3104 MET cc_start: 0.8552 (ppp) cc_final: 0.8222 (ppp) REVERT: A 3159 LEU cc_start: 0.9351 (mm) cc_final: 0.8706 (pp) REVERT: A 3981 MET cc_start: 0.8926 (tmm) cc_final: 0.8498 (tmm) REVERT: A 4048 PHE cc_start: 0.9137 (t80) cc_final: 0.8481 (t80) REVERT: A 4268 MET cc_start: 0.6133 (tmm) cc_final: 0.5822 (tmm) REVERT: A 4804 MET cc_start: 0.8823 (mmm) cc_final: 0.8288 (mmm) REVERT: G 6 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7626 (mt-10) REVERT: G 50 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8172 (ttp-110) REVERT: D 81 MET cc_start: 0.8384 (tmm) cc_final: 0.7893 (tmm) REVERT: D 128 MET cc_start: 0.8582 (mtp) cc_final: 0.8367 (mtp) REVERT: D 956 HIS cc_start: 0.9038 (t70) cc_final: 0.8758 (t70) REVERT: D 1165 MET cc_start: 0.8269 (mtp) cc_final: 0.7902 (mtp) REVERT: D 1215 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: D 1494 MET cc_start: 0.7765 (tmm) cc_final: 0.7558 (tmm) REVERT: D 1831 MET cc_start: 0.8953 (mtp) cc_final: 0.8672 (mtt) REVERT: D 2084 MET cc_start: 0.8923 (mtp) cc_final: 0.8649 (mtm) REVERT: D 2142 MET cc_start: 0.8458 (tpt) cc_final: 0.8171 (tpp) REVERT: D 2162 MET cc_start: 0.8607 (mmp) cc_final: 0.8384 (mmp) REVERT: D 2347 MET cc_start: 0.8445 (mmp) cc_final: 0.7943 (mmp) REVERT: D 2534 LEU cc_start: 0.9084 (mt) cc_final: 0.8668 (tp) REVERT: D 2681 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7910 (mmm) REVERT: D 2688 MET cc_start: 0.1002 (ptt) cc_final: 0.0628 (ptt) REVERT: D 2719 TYR cc_start: 0.8671 (t80) cc_final: 0.8283 (t80) REVERT: D 2720 PHE cc_start: 0.8605 (t80) cc_final: 0.8108 (t80) REVERT: D 2724 TYR cc_start: 0.8731 (t80) cc_final: 0.8403 (t80) REVERT: D 2771 TYR cc_start: 0.8455 (m-10) cc_final: 0.7795 (m-10) REVERT: D 2782 MET cc_start: 0.8831 (ttp) cc_final: 0.8430 (tmm) REVERT: D 2932 TYR cc_start: 0.8635 (t80) cc_final: 0.8259 (t80) REVERT: D 2944 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6419 (m-30) REVERT: D 3072 MET cc_start: 0.8977 (mmm) cc_final: 0.8315 (mmm) REVERT: D 3104 MET cc_start: 0.8539 (ppp) cc_final: 0.8141 (ppp) REVERT: D 3134 LEU cc_start: 0.9272 (mt) cc_final: 0.9014 (mt) REVERT: D 3322 LEU cc_start: 0.8775 (tt) cc_final: 0.8353 (mt) REVERT: D 3323 MET cc_start: 0.8618 (mmm) cc_final: 0.8127 (mmt) REVERT: D 3819 MET cc_start: 0.6758 (ptp) cc_final: 0.6453 (ptp) REVERT: B 81 MET cc_start: 0.8202 (tmm) cc_final: 0.7784 (tmm) REVERT: B 399 MET cc_start: 0.7581 (tmm) cc_final: 0.7204 (tmm) REVERT: B 940 LEU cc_start: 0.9380 (mt) cc_final: 0.9104 (mt) REVERT: B 956 HIS cc_start: 0.9098 (t70) cc_final: 0.8835 (t70) REVERT: B 1035 TYR cc_start: 0.7804 (t80) cc_final: 0.7382 (t80) REVERT: B 1165 MET cc_start: 0.8209 (mtp) cc_final: 0.7821 (mtp) REVERT: B 1168 MET cc_start: 0.8621 (mmm) cc_final: 0.8118 (mmm) REVERT: B 1421 MET cc_start: 0.8811 (mmp) cc_final: 0.8609 (mmm) REVERT: B 1494 MET cc_start: 0.7704 (tmm) cc_final: 0.7438 (tmm) REVERT: B 1831 MET cc_start: 0.8815 (mtp) cc_final: 0.8583 (mtp) REVERT: B 1906 MET cc_start: 0.8477 (mmm) cc_final: 0.8149 (mmm) REVERT: B 2066 MET cc_start: 0.8759 (mmp) cc_final: 0.8312 (mmm) REVERT: B 2234 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7814 (mtp) REVERT: B 2279 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8467 (ptp) REVERT: B 2347 MET cc_start: 0.8205 (mmp) cc_final: 0.7723 (mmp) REVERT: B 2384 MET cc_start: 0.8598 (mpp) cc_final: 0.8334 (mpp) REVERT: B 2493 LEU cc_start: 0.9065 (mm) cc_final: 0.8858 (mp) REVERT: B 2719 TYR cc_start: 0.8568 (t80) cc_final: 0.8287 (t80) REVERT: B 2720 PHE cc_start: 0.8657 (t80) cc_final: 0.8287 (t80) REVERT: B 2843 MET cc_start: 0.7839 (ppp) cc_final: 0.7392 (ppp) REVERT: B 2844 MET cc_start: 0.8750 (ppp) cc_final: 0.8390 (ppp) REVERT: B 2858 MET cc_start: 0.8907 (mpp) cc_final: 0.8638 (pmm) REVERT: B 2932 TYR cc_start: 0.8330 (t80) cc_final: 0.7934 (t80) REVERT: B 3109 PHE cc_start: 0.8790 (m-10) cc_final: 0.8508 (m-10) REVERT: B 3241 MET cc_start: 0.8948 (mtp) cc_final: 0.8697 (mtp) REVERT: B 3246 MET cc_start: 0.8619 (tmm) cc_final: 0.8388 (tmm) REVERT: B 3978 MET cc_start: 0.8998 (ttp) cc_final: 0.8753 (ttt) REVERT: B 4048 PHE cc_start: 0.8720 (m-80) cc_final: 0.8367 (m-80) REVERT: B 4052 MET cc_start: 0.8550 (mtp) cc_final: 0.8073 (ttm) REVERT: B 4268 MET cc_start: 0.6402 (tmm) cc_final: 0.6088 (tmm) REVERT: B 4292 MET cc_start: 0.8182 (mmm) cc_final: 0.7837 (mmm) REVERT: B 4748 MET cc_start: 0.7145 (mpp) cc_final: 0.6942 (mpp) REVERT: B 4943 MET cc_start: 0.8820 (mtp) cc_final: 0.8410 (mtp) REVERT: C 81 MET cc_start: 0.8329 (tmm) cc_final: 0.7916 (tmm) REVERT: C 128 MET cc_start: 0.8675 (mtp) cc_final: 0.8416 (mtp) REVERT: C 349 MET cc_start: 0.8480 (mmm) cc_final: 0.8236 (mmt) REVERT: C 399 MET cc_start: 0.7590 (tmm) cc_final: 0.7285 (tmm) REVERT: C 956 HIS cc_start: 0.9250 (t70) cc_final: 0.8990 (t70) REVERT: C 995 MET cc_start: 0.8085 (mtt) cc_final: 0.7610 (mpp) REVERT: C 1165 MET cc_start: 0.8252 (mtp) cc_final: 0.7731 (mtp) REVERT: C 1494 MET cc_start: 0.7505 (tmm) cc_final: 0.7193 (tmm) REVERT: C 1948 MET cc_start: 0.7990 (mmp) cc_final: 0.7658 (mmm) REVERT: C 2066 MET cc_start: 0.8784 (mmt) cc_final: 0.8421 (mmm) REVERT: C 2279 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8367 (tmm) REVERT: C 2347 MET cc_start: 0.8389 (mmt) cc_final: 0.7929 (mmp) REVERT: C 2384 MET cc_start: 0.8558 (mpp) cc_final: 0.8226 (mpp) REVERT: C 2669 LEU cc_start: 0.9285 (mt) cc_final: 0.9044 (tp) REVERT: C 2681 MET cc_start: 0.8585 (tpt) cc_final: 0.7845 (tpt) REVERT: C 2719 TYR cc_start: 0.8629 (t80) cc_final: 0.8270 (t80) REVERT: C 2720 PHE cc_start: 0.8722 (t80) cc_final: 0.8302 (t80) REVERT: C 2840 MET cc_start: 0.9022 (ptm) cc_final: 0.8238 (mmt) REVERT: C 2843 MET cc_start: 0.8151 (ppp) cc_final: 0.7605 (ppp) REVERT: C 2844 MET cc_start: 0.8781 (ppp) cc_final: 0.8537 (ppp) REVERT: C 2932 TYR cc_start: 0.8586 (t80) cc_final: 0.8102 (t80) REVERT: C 2944 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: C 3022 PHE cc_start: 0.8450 (m-10) cc_final: 0.8013 (m-10) REVERT: C 3131 TYR cc_start: 0.8577 (m-10) cc_final: 0.8073 (m-10) REVERT: C 3263 MET cc_start: 0.8193 (tmm) cc_final: 0.7980 (tpt) REVERT: C 3322 LEU cc_start: 0.8656 (tt) cc_final: 0.8169 (mt) REVERT: C 3323 MET cc_start: 0.8569 (mmp) cc_final: 0.8271 (mmt) REVERT: C 3981 MET cc_start: 0.8892 (tmm) cc_final: 0.8420 (ttm) REVERT: C 4279 MET cc_start: 0.7296 (mmm) cc_final: 0.7069 (mtm) REVERT: C 4306 PHE cc_start: 0.6718 (m-10) cc_final: 0.6489 (t80) REVERT: C 4748 MET cc_start: 0.7163 (mpp) cc_final: 0.6509 (mpp) REVERT: C 4943 MET cc_start: 0.8765 (mtp) cc_final: 0.8347 (mtp) outliers start: 91 outliers final: 66 residues processed: 855 average time/residue: 1.1914 time to fit residues: 1813.8066 Evaluate side-chains 857 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 782 time to evaluate : 12.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1794 MET Chi-restraints excluded: chain A residue 2167 MET Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3821 THR Chi-restraints excluded: chain A residue 4258 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2944 ASP Chi-restraints excluded: chain D residue 3075 LEU Chi-restraints excluded: chain D residue 3821 THR Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2186 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 3821 THR Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 1.9990 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 8.9990 chunk 501 optimal weight: 4.9990 chunk 327 optimal weight: 0.0170 chunk 322 optimal weight: 10.0000 chunk 1058 optimal weight: 2.9990 chunk 1134 optimal weight: 30.0000 chunk 823 optimal weight: 0.0370 chunk 155 optimal weight: 1.9990 chunk 1309 optimal weight: 9.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3274 ASN A3811 GLN A4488 GLN E 26 HIS F 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1562 ASN ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4488 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2727 HIS ** B2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3031 ASN ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3665 HIS ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3031 ASN ** C3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4488 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 141628 Z= 0.166 Angle : 0.608 17.262 191356 Z= 0.301 Chirality : 0.041 0.407 20988 Planarity : 0.004 0.073 24588 Dihedral : 5.325 67.714 19028 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 7.99 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.66 (0.07), residues: 17212 helix: 1.33 (0.06), residues: 8740 sheet: -0.21 (0.13), residues: 1744 loop : -0.49 (0.08), residues: 6728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 893 HIS 0.013 0.001 HIS D2410 PHE 0.027 0.001 PHE C3162 TYR 0.030 0.001 TYR B2939 ARG 0.015 0.000 ARG D1960 *********************** 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 872 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 788 time to evaluate : 12.503 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: H 4 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6756 (tm-30) REVERT: A 81 MET cc_start: 0.8274 (tmm) cc_final: 0.7788 (tmm) REVERT: A 399 MET cc_start: 0.7619 (tmm) cc_final: 0.7342 (tmm) REVERT: A 403 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 940 LEU cc_start: 0.9391 (mt) cc_final: 0.9146 (mt) REVERT: A 956 HIS cc_start: 0.8983 (t70) cc_final: 0.8705 (t70) REVERT: A 981 MET cc_start: 0.7380 (tmm) cc_final: 0.7009 (tpt) REVERT: A 1494 MET cc_start: 0.7740 (tmm) cc_final: 0.7500 (tmm) REVERT: A 1694 MET cc_start: 0.8874 (tpp) cc_final: 0.8662 (tpp) REVERT: A 2142 MET cc_start: 0.8370 (tpt) cc_final: 0.8051 (tpp) REVERT: A 2347 MET cc_start: 0.8093 (mmp) cc_final: 0.7698 (mmp) REVERT: A 2493 LEU cc_start: 0.9011 (mm) cc_final: 0.8800 (mp) REVERT: A 2534 LEU cc_start: 0.9198 (mt) cc_final: 0.8853 (tp) REVERT: A 2553 TYR cc_start: 0.7821 (t80) cc_final: 0.7295 (t80) REVERT: A 2614 TYR cc_start: 0.8742 (m-10) cc_final: 0.8525 (m-10) REVERT: A 2681 MET cc_start: 0.8505 (tpt) cc_final: 0.8266 (mmm) REVERT: A 2695 MET cc_start: 0.6558 (pmm) cc_final: 0.6271 (pmm) REVERT: A 2719 TYR cc_start: 0.8574 (t80) cc_final: 0.8134 (t80) REVERT: A 2720 PHE cc_start: 0.8528 (t80) cc_final: 0.8121 (t80) REVERT: A 2828 MET cc_start: 0.6988 (pmm) cc_final: 0.6507 (mtp) REVERT: A 2840 MET cc_start: 0.8562 (mmm) cc_final: 0.8345 (tpt) REVERT: A 2932 TYR cc_start: 0.8446 (t80) cc_final: 0.8034 (t80) REVERT: A 3022 PHE cc_start: 0.8266 (m-10) cc_final: 0.7953 (m-10) REVERT: A 3072 MET cc_start: 0.8985 (mmp) cc_final: 0.8211 (mmm) REVERT: A 3104 MET cc_start: 0.8527 (ppp) cc_final: 0.8189 (ppp) REVERT: A 3159 LEU cc_start: 0.9338 (mm) cc_final: 0.8153 (pp) REVERT: A 3241 MET cc_start: 0.8883 (mtp) cc_final: 0.8670 (mmm) REVERT: A 3981 MET cc_start: 0.8884 (tmm) cc_final: 0.8497 (tmm) REVERT: A 4048 PHE cc_start: 0.9109 (t80) cc_final: 0.8450 (t80) REVERT: A 4268 MET cc_start: 0.6189 (tmm) cc_final: 0.5903 (tmm) REVERT: A 4274 MET cc_start: 0.5618 (tmm) cc_final: 0.4149 (ptp) REVERT: G 53 LYS cc_start: 0.9236 (mmtm) cc_final: 0.9033 (mmtp) REVERT: D 81 MET cc_start: 0.8356 (tmm) cc_final: 0.7872 (tmm) REVERT: D 778 MET cc_start: 0.8198 (ptp) cc_final: 0.7842 (ptm) REVERT: D 956 HIS cc_start: 0.9011 (t70) cc_final: 0.8727 (t70) REVERT: D 1165 MET cc_start: 0.8287 (mtp) cc_final: 0.7934 (mtp) REVERT: D 1215 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8058 (mtt) REVERT: D 1494 MET cc_start: 0.7755 (tmm) cc_final: 0.7549 (tmm) REVERT: D 1831 MET cc_start: 0.8901 (mtp) cc_final: 0.8629 (mtt) REVERT: D 2142 MET cc_start: 0.8416 (tpt) cc_final: 0.8131 (tpp) REVERT: D 2347 MET cc_start: 0.8436 (mmp) cc_final: 0.7942 (mmp) REVERT: D 2534 LEU cc_start: 0.9056 (mt) cc_final: 0.8665 (tp) REVERT: D 2681 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7892 (mmm) REVERT: D 2688 MET cc_start: 0.1065 (ptt) cc_final: 0.0720 (ptt) REVERT: D 2695 MET cc_start: 0.5907 (pmm) cc_final: 0.5659 (pmm) REVERT: D 2719 TYR cc_start: 0.8665 (t80) cc_final: 0.8261 (t80) REVERT: D 2720 PHE cc_start: 0.8596 (t80) cc_final: 0.8100 (t80) REVERT: D 2724 TYR cc_start: 0.8661 (t80) cc_final: 0.8334 (t80) REVERT: D 2771 TYR cc_start: 0.8420 (m-10) cc_final: 0.7864 (m-10) REVERT: D 2782 MET cc_start: 0.8770 (ttp) cc_final: 0.8412 (tmm) REVERT: D 2798 MET cc_start: 0.7976 (mmp) cc_final: 0.7611 (mmp) REVERT: D 2932 TYR cc_start: 0.8595 (t80) cc_final: 0.8206 (t80) REVERT: D 2944 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: D 3072 MET cc_start: 0.8969 (mmm) cc_final: 0.8325 (mmm) REVERT: D 3104 MET cc_start: 0.8521 (ppp) cc_final: 0.8222 (tmm) REVERT: D 3134 LEU cc_start: 0.9259 (mt) cc_final: 0.8964 (mt) REVERT: D 3273 MET cc_start: 0.9252 (ppp) cc_final: 0.8863 (ppp) REVERT: D 3322 LEU cc_start: 0.8733 (tt) cc_final: 0.8309 (mt) REVERT: D 3323 MET cc_start: 0.8588 (mmm) cc_final: 0.8135 (mmt) REVERT: D 3819 MET cc_start: 0.6706 (ptp) cc_final: 0.6415 (ptp) REVERT: D 4943 MET cc_start: 0.8785 (mtp) cc_final: 0.8305 (mtp) REVERT: B 81 MET cc_start: 0.8168 (tmm) cc_final: 0.7742 (tmm) REVERT: B 399 MET cc_start: 0.7562 (tmm) cc_final: 0.7227 (tmm) REVERT: B 940 LEU cc_start: 0.9346 (mt) cc_final: 0.9077 (mt) REVERT: B 956 HIS cc_start: 0.9086 (t70) cc_final: 0.8822 (t70) REVERT: B 1035 TYR cc_start: 0.7744 (t80) cc_final: 0.7363 (t80) REVERT: B 1165 MET cc_start: 0.8185 (mtp) cc_final: 0.7793 (mtp) REVERT: B 1168 MET cc_start: 0.8610 (mmm) cc_final: 0.8061 (mmm) REVERT: B 1421 MET cc_start: 0.8811 (mmp) cc_final: 0.8605 (mmm) REVERT: B 1494 MET cc_start: 0.7736 (tmm) cc_final: 0.7476 (tmm) REVERT: B 2066 MET cc_start: 0.8761 (mmp) cc_final: 0.8212 (mmm) REVERT: B 2347 MET cc_start: 0.8173 (mmp) cc_final: 0.7711 (mmp) REVERT: B 2384 MET cc_start: 0.8536 (mpp) cc_final: 0.8293 (mpp) REVERT: B 2493 LEU cc_start: 0.9017 (mm) cc_final: 0.8810 (mp) REVERT: B 2585 MET cc_start: 0.7677 (pmm) cc_final: 0.6861 (pmm) REVERT: B 2719 TYR cc_start: 0.8592 (t80) cc_final: 0.8320 (t80) REVERT: B 2720 PHE cc_start: 0.8616 (t80) cc_final: 0.8258 (t80) REVERT: B 2840 MET cc_start: 0.8169 (mmm) cc_final: 0.7608 (mmm) REVERT: B 2843 MET cc_start: 0.7880 (ppp) cc_final: 0.7420 (ppp) REVERT: B 2844 MET cc_start: 0.8671 (ppp) cc_final: 0.8376 (ppp) REVERT: B 2932 TYR cc_start: 0.8311 (t80) cc_final: 0.7908 (t80) REVERT: B 2944 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6525 (m-30) REVERT: B 3109 PHE cc_start: 0.8790 (m-10) cc_final: 0.8510 (m-10) REVERT: B 3241 MET cc_start: 0.8925 (mtp) cc_final: 0.8678 (mtp) REVERT: B 3246 MET cc_start: 0.8588 (tmm) cc_final: 0.8364 (tmm) REVERT: B 3819 MET cc_start: 0.6208 (pmm) cc_final: 0.5097 (pmm) REVERT: B 3978 MET cc_start: 0.8970 (ttp) cc_final: 0.8733 (ttt) REVERT: B 4048 PHE cc_start: 0.8715 (m-80) cc_final: 0.8341 (m-80) REVERT: B 4052 MET cc_start: 0.8522 (mtp) cc_final: 0.8055 (ttm) REVERT: B 4256 MET cc_start: 0.8266 (mmt) cc_final: 0.7955 (mmm) REVERT: B 4268 MET cc_start: 0.6447 (tmm) cc_final: 0.6134 (tmm) REVERT: B 4943 MET cc_start: 0.8768 (mtp) cc_final: 0.8318 (mtp) REVERT: C 81 MET cc_start: 0.8295 (tmm) cc_final: 0.7872 (tmm) REVERT: C 128 MET cc_start: 0.8616 (mtp) cc_final: 0.8394 (mtp) REVERT: C 349 MET cc_start: 0.8443 (mmm) cc_final: 0.8190 (mmt) REVERT: C 399 MET cc_start: 0.7559 (tmm) cc_final: 0.7275 (tmm) REVERT: C 956 HIS cc_start: 0.9219 (t70) cc_final: 0.8954 (t70) REVERT: C 1165 MET cc_start: 0.8234 (mtp) cc_final: 0.7704 (mtp) REVERT: C 1494 MET cc_start: 0.7496 (tmm) cc_final: 0.7190 (tmm) REVERT: C 1948 MET cc_start: 0.7950 (mmp) cc_final: 0.7662 (mmm) REVERT: C 2066 MET cc_start: 0.8784 (mmt) cc_final: 0.8432 (mmm) REVERT: C 2279 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8439 (ppp) REVERT: C 2347 MET cc_start: 0.8377 (mmt) cc_final: 0.7933 (mmp) REVERT: C 2384 MET cc_start: 0.8528 (mpp) cc_final: 0.8209 (mpp) REVERT: C 2719 TYR cc_start: 0.8623 (t80) cc_final: 0.8264 (t80) REVERT: C 2720 PHE cc_start: 0.8711 (t80) cc_final: 0.8297 (t80) REVERT: C 2840 MET cc_start: 0.9018 (ptm) cc_final: 0.8243 (mmt) REVERT: C 2843 MET cc_start: 0.8129 (ppp) cc_final: 0.7588 (ppp) REVERT: C 2844 MET cc_start: 0.8746 (ppp) cc_final: 0.8514 (ppp) REVERT: C 2858 MET cc_start: 0.9050 (mpp) cc_final: 0.8766 (pmm) REVERT: C 2932 TYR cc_start: 0.8586 (t80) cc_final: 0.8087 (t80) REVERT: C 2944 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: C 3022 PHE cc_start: 0.8389 (m-10) cc_final: 0.7938 (m-10) REVERT: C 3263 MET cc_start: 0.8117 (tmm) cc_final: 0.7885 (tpt) REVERT: C 3322 LEU cc_start: 0.8543 (tt) cc_final: 0.8074 (mt) REVERT: C 3323 MET cc_start: 0.8529 (mmp) cc_final: 0.8232 (mmt) REVERT: C 3981 MET cc_start: 0.8899 (tmm) cc_final: 0.8550 (tmm) REVERT: C 4707 MET cc_start: 0.8044 (ttt) cc_final: 0.7833 (ttm) REVERT: C 4748 MET cc_start: 0.7084 (mpp) cc_final: 0.6488 (mpp) REVERT: C 4943 MET cc_start: 0.8727 (mtp) cc_final: 0.8329 (mtp) outliers start: 84 outliers final: 57 residues processed: 838 average time/residue: 1.2122 time to fit residues: 1798.5242 Evaluate side-chains 843 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 779 time to evaluate : 12.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3821 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2456 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2944 ASP Chi-restraints excluded: chain D residue 3075 LEU Chi-restraints excluded: chain D residue 3821 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 2944 ASP Chi-restraints excluded: chain B residue 3111 HIS Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2186 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2456 MET Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 3111 HIS Chi-restraints excluded: chain C residue 3821 THR Chi-restraints excluded: chain C residue 4258 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 7.9990 chunk 1595 optimal weight: 6.9990 chunk 1455 optimal weight: 9.9990 chunk 1552 optimal weight: 40.0000 chunk 934 optimal weight: 8.9990 chunk 676 optimal weight: 3.9990 chunk 1218 optimal weight: 9.9990 chunk 476 optimal weight: 9.9990 chunk 1402 optimal weight: 20.0000 chunk 1467 optimal weight: 8.9990 chunk 1546 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: H 26 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4488 GLN E 26 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4488 GLN ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1631 HIS ** B2540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3318 HIS ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4488 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 141628 Z= 0.408 Angle : 0.674 18.760 191356 Z= 0.339 Chirality : 0.044 0.449 20988 Planarity : 0.005 0.125 24588 Dihedral : 5.413 75.908 19028 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 0.61 % Allowed : 8.13 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.63 (0.07), residues: 17212 helix: 1.36 (0.06), residues: 8704 sheet: -0.31 (0.12), residues: 1756 loop : -0.54 (0.08), residues: 6752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 893 HIS 0.016 0.001 HIS F 26 PHE 0.034 0.002 PHE D3170 TYR 0.030 0.002 TYR B2939 ARG 0.008 0.001 ARG F 50 *********************** 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 882 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 798 time to evaluate : 12.292 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: H 4 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6787 (tm-30) REVERT: H 67 MET cc_start: 0.8598 (mtp) cc_final: 0.8231 (mtp) REVERT: A 81 MET cc_start: 0.8310 (tmm) cc_final: 0.7834 (tmm) REVERT: A 399 MET cc_start: 0.7632 (tmm) cc_final: 0.7355 (tmm) REVERT: A 403 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 940 LEU cc_start: 0.9411 (mt) cc_final: 0.9177 (mt) REVERT: A 1165 MET cc_start: 0.8201 (mtp) cc_final: 0.7628 (mtp) REVERT: A 1494 MET cc_start: 0.7844 (tmm) cc_final: 0.7573 (tmm) REVERT: A 1948 MET cc_start: 0.7962 (mmp) cc_final: 0.7627 (mmm) REVERT: A 2066 MET cc_start: 0.8687 (mmp) cc_final: 0.8263 (mmm) REVERT: A 2142 MET cc_start: 0.8402 (tpt) cc_final: 0.8062 (tpp) REVERT: A 2347 MET cc_start: 0.8260 (mmp) cc_final: 0.7828 (mmp) REVERT: A 2493 LEU cc_start: 0.9073 (mm) cc_final: 0.8863 (mp) REVERT: A 2534 LEU cc_start: 0.9223 (mt) cc_final: 0.8843 (tp) REVERT: A 2681 MET cc_start: 0.8620 (tpt) cc_final: 0.7738 (tpp) REVERT: A 2719 TYR cc_start: 0.8610 (t80) cc_final: 0.8179 (t80) REVERT: A 2828 MET cc_start: 0.7049 (pmm) cc_final: 0.6599 (mtt) REVERT: A 2858 MET cc_start: 0.9039 (mpp) cc_final: 0.8559 (pmm) REVERT: A 2932 TYR cc_start: 0.8485 (t80) cc_final: 0.8059 (t80) REVERT: A 3022 PHE cc_start: 0.8382 (m-10) cc_final: 0.8070 (m-10) REVERT: A 3072 MET cc_start: 0.9022 (mmp) cc_final: 0.8260 (mmm) REVERT: A 3104 MET cc_start: 0.8572 (ppp) cc_final: 0.8232 (ppp) REVERT: A 3159 LEU cc_start: 0.9373 (mm) cc_final: 0.8815 (pp) REVERT: A 3981 MET cc_start: 0.8935 (tmm) cc_final: 0.8498 (tmm) REVERT: A 4048 PHE cc_start: 0.9151 (t80) cc_final: 0.8534 (t80) REVERT: A 4268 MET cc_start: 0.6185 (tmm) cc_final: 0.5847 (tmm) REVERT: A 4274 MET cc_start: 0.5533 (tmm) cc_final: 0.4080 (ptp) REVERT: A 4804 MET cc_start: 0.8725 (mmm) cc_final: 0.8387 (mmm) REVERT: G 6 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7528 (mt-10) REVERT: D 81 MET cc_start: 0.8405 (tmm) cc_final: 0.7940 (tmm) REVERT: D 778 MET cc_start: 0.8215 (ptp) cc_final: 0.7868 (ptm) REVERT: D 940 LEU cc_start: 0.9362 (mt) cc_final: 0.9122 (mt) REVERT: D 1165 MET cc_start: 0.8288 (mtp) cc_final: 0.7916 (mtp) REVERT: D 1215 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (mtt) REVERT: D 1494 MET cc_start: 0.7820 (tmm) cc_final: 0.7588 (tmm) REVERT: D 2084 MET cc_start: 0.8885 (mtp) cc_final: 0.8592 (mtp) REVERT: D 2142 MET cc_start: 0.8463 (tpt) cc_final: 0.8175 (tpp) REVERT: D 2347 MET cc_start: 0.8557 (mmp) cc_final: 0.8057 (mmp) REVERT: D 2534 LEU cc_start: 0.9087 (mt) cc_final: 0.8672 (tp) REVERT: D 2652 LEU cc_start: 0.9037 (mp) cc_final: 0.8813 (mm) REVERT: D 2681 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: D 2688 MET cc_start: 0.1167 (ptt) cc_final: 0.0807 (ptt) REVERT: D 2719 TYR cc_start: 0.8683 (t80) cc_final: 0.8267 (t80) REVERT: D 2720 PHE cc_start: 0.8621 (t80) cc_final: 0.8108 (t80) REVERT: D 2724 TYR cc_start: 0.8702 (t80) cc_final: 0.8459 (t80) REVERT: D 2782 MET cc_start: 0.8777 (ttp) cc_final: 0.8420 (tmm) REVERT: D 2932 TYR cc_start: 0.8629 (t80) cc_final: 0.8232 (t80) REVERT: D 2944 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: D 3022 PHE cc_start: 0.8177 (m-10) cc_final: 0.7770 (m-10) REVERT: D 3072 MET cc_start: 0.8991 (mmm) cc_final: 0.8478 (mmm) REVERT: D 3104 MET cc_start: 0.8566 (ppp) cc_final: 0.8290 (tmm) REVERT: D 3134 LEU cc_start: 0.9278 (mt) cc_final: 0.8972 (mt) REVERT: D 3170 PHE cc_start: 0.7611 (p90) cc_final: 0.7320 (p90) REVERT: D 3273 MET cc_start: 0.9280 (ppp) cc_final: 0.8924 (ppp) REVERT: D 3322 LEU cc_start: 0.8774 (tt) cc_final: 0.8459 (mt) REVERT: D 3819 MET cc_start: 0.6757 (ptp) cc_final: 0.6450 (ptp) REVERT: D 4480 PHE cc_start: 0.4923 (t80) cc_final: 0.4637 (t80) REVERT: D 4943 MET cc_start: 0.8840 (mtp) cc_final: 0.8348 (mtp) REVERT: B 81 MET cc_start: 0.8231 (tmm) cc_final: 0.7833 (tmm) REVERT: B 241 MET cc_start: 0.5599 (mmp) cc_final: 0.5390 (mmp) REVERT: B 399 MET cc_start: 0.7618 (tmm) cc_final: 0.7294 (tmm) REVERT: B 940 LEU cc_start: 0.9378 (mt) cc_final: 0.9103 (mt) REVERT: B 956 HIS cc_start: 0.9092 (t70) cc_final: 0.8826 (t70) REVERT: B 1165 MET cc_start: 0.8235 (mtp) cc_final: 0.7860 (mtp) REVERT: B 1168 MET cc_start: 0.8641 (mmm) cc_final: 0.8104 (mmm) REVERT: B 1494 MET cc_start: 0.7786 (tmm) cc_final: 0.7502 (tmm) REVERT: B 2066 MET cc_start: 0.8764 (mmp) cc_final: 0.8213 (mmm) REVERT: B 2279 MET cc_start: 0.8627 (ptp) cc_final: 0.8366 (ppp) REVERT: B 2347 MET cc_start: 0.8307 (mmp) cc_final: 0.7816 (mmp) REVERT: B 2384 MET cc_start: 0.8645 (mpp) cc_final: 0.8365 (mpp) REVERT: B 2493 LEU cc_start: 0.9098 (mm) cc_final: 0.8891 (mp) REVERT: B 2719 TYR cc_start: 0.8585 (t80) cc_final: 0.8298 (t80) REVERT: B 2720 PHE cc_start: 0.8657 (t80) cc_final: 0.8286 (t80) REVERT: B 2734 MET cc_start: 0.7278 (mpp) cc_final: 0.6539 (mpp) REVERT: B 2843 MET cc_start: 0.7869 (ppp) cc_final: 0.7458 (ppp) REVERT: B 2844 MET cc_start: 0.8735 (ppp) cc_final: 0.8407 (ppp) REVERT: B 2858 MET cc_start: 0.8911 (mpp) cc_final: 0.8651 (pmm) REVERT: B 2932 TYR cc_start: 0.8327 (t80) cc_final: 0.7926 (t80) REVERT: B 2944 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: B 3022 PHE cc_start: 0.8355 (m-80) cc_final: 0.8017 (m-10) REVERT: B 3072 MET cc_start: 0.8923 (mmm) cc_final: 0.8506 (mmm) REVERT: B 3104 MET cc_start: 0.8818 (ptm) cc_final: 0.8431 (ptt) REVERT: B 3109 PHE cc_start: 0.8829 (m-10) cc_final: 0.8552 (m-10) REVERT: B 3241 MET cc_start: 0.8964 (mtp) cc_final: 0.8721 (mtp) REVERT: B 3246 MET cc_start: 0.8637 (tmm) cc_final: 0.8423 (tmm) REVERT: B 3978 MET cc_start: 0.9009 (ttp) cc_final: 0.8768 (ttt) REVERT: B 4048 PHE cc_start: 0.8735 (m-80) cc_final: 0.8336 (m-80) REVERT: B 4052 MET cc_start: 0.8591 (mtp) cc_final: 0.8087 (ttm) REVERT: B 4256 MET cc_start: 0.8260 (mmt) cc_final: 0.7974 (mmm) REVERT: B 4268 MET cc_start: 0.6416 (tmm) cc_final: 0.6123 (tmm) REVERT: B 4943 MET cc_start: 0.8824 (mtp) cc_final: 0.8415 (mtp) REVERT: C 81 MET cc_start: 0.8319 (tmm) cc_final: 0.7921 (tmm) REVERT: C 128 MET cc_start: 0.8673 (mtp) cc_final: 0.8400 (mtp) REVERT: C 241 MET cc_start: 0.5607 (mmp) cc_final: 0.5403 (mmp) REVERT: C 349 MET cc_start: 0.8509 (mmm) cc_final: 0.8277 (mmt) REVERT: C 399 MET cc_start: 0.7600 (tmm) cc_final: 0.7303 (tmm) REVERT: C 956 HIS cc_start: 0.9245 (t70) cc_final: 0.8985 (t70) REVERT: C 1165 MET cc_start: 0.8267 (mtp) cc_final: 0.7853 (mtp) REVERT: C 1494 MET cc_start: 0.7520 (tmm) cc_final: 0.7212 (tmm) REVERT: C 1948 MET cc_start: 0.7967 (mmp) cc_final: 0.7656 (mmm) REVERT: C 2066 MET cc_start: 0.8776 (mmt) cc_final: 0.8421 (mmm) REVERT: C 2279 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (tmm) REVERT: C 2347 MET cc_start: 0.8530 (mmt) cc_final: 0.8102 (mmp) REVERT: C 2384 MET cc_start: 0.8600 (mpp) cc_final: 0.8296 (mpp) REVERT: C 2652 LEU cc_start: 0.8913 (mp) cc_final: 0.8621 (mm) REVERT: C 2669 LEU cc_start: 0.9290 (mt) cc_final: 0.9030 (tp) REVERT: C 2681 MET cc_start: 0.8576 (tpt) cc_final: 0.7837 (tpt) REVERT: C 2719 TYR cc_start: 0.8653 (t80) cc_final: 0.8301 (t80) REVERT: C 2720 PHE cc_start: 0.8735 (t80) cc_final: 0.8309 (t80) REVERT: C 2840 MET cc_start: 0.9056 (ptm) cc_final: 0.8337 (mmm) REVERT: C 2843 MET cc_start: 0.8158 (ppp) cc_final: 0.7697 (ppp) REVERT: C 2844 MET cc_start: 0.8794 (ppp) cc_final: 0.8548 (ppp) REVERT: C 2932 TYR cc_start: 0.8593 (t80) cc_final: 0.8090 (t80) REVERT: C 2944 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6491 (m-30) REVERT: C 3022 PHE cc_start: 0.8469 (m-10) cc_final: 0.7998 (m-10) REVERT: C 3072 MET cc_start: 0.8630 (mmt) cc_final: 0.8234 (mmm) REVERT: C 3131 TYR cc_start: 0.8571 (m-10) cc_final: 0.8060 (m-10) REVERT: C 3159 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 3263 MET cc_start: 0.8176 (tmm) cc_final: 0.7945 (tpt) REVERT: C 3285 TYR cc_start: 0.7216 (m-10) cc_final: 0.6997 (m-10) REVERT: C 3322 LEU cc_start: 0.8654 (tt) cc_final: 0.8236 (mt) REVERT: C 3323 MET cc_start: 0.8595 (mmp) cc_final: 0.8311 (mmt) REVERT: C 3981 MET cc_start: 0.8886 (tmm) cc_final: 0.8437 (ttm) REVERT: C 4274 MET cc_start: 0.5559 (ttt) cc_final: 0.4573 (mmm) REVERT: C 4748 MET cc_start: 0.7161 (mpp) cc_final: 0.6475 (mpp) REVERT: C 4943 MET cc_start: 0.8780 (mtp) cc_final: 0.8364 (mtp) outliers start: 84 outliers final: 66 residues processed: 854 average time/residue: 1.1800 time to fit residues: 1794.2527 Evaluate side-chains 862 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 788 time to evaluate : 12.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1794 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2905 ARG Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3236 GLU Chi-restraints excluded: chain A residue 3821 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2448 ASP Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2944 ASP Chi-restraints excluded: chain D residue 3075 LEU Chi-restraints excluded: chain D residue 3821 THR Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain D residue 4752 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 2944 ASP Chi-restraints excluded: chain B residue 3111 HIS Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2186 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 3111 HIS Chi-restraints excluded: chain C residue 3159 LEU Chi-restraints excluded: chain C residue 3821 THR Chi-restraints excluded: chain C residue 4258 MET Chi-restraints excluded: chain C residue 4752 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 8.9990 chunk 1641 optimal weight: 3.9990 chunk 1001 optimal weight: 4.9990 chunk 778 optimal weight: 1.9990 chunk 1140 optimal weight: 9.9990 chunk 1721 optimal weight: 1.9990 chunk 1584 optimal weight: 0.0980 chunk 1370 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 1058 optimal weight: 2.9990 chunk 840 optimal weight: 0.9980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4488 GLN E 26 HIS F 26 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN D3811 GLN D4488 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3274 ASN ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4488 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 141628 Z= 0.175 Angle : 0.622 17.662 191356 Z= 0.308 Chirality : 0.041 0.414 20988 Planarity : 0.004 0.076 24588 Dihedral : 5.264 68.096 19028 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 0.56 % Allowed : 8.34 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.78 (0.07), residues: 17212 helix: 1.44 (0.06), residues: 8752 sheet: -0.18 (0.13), residues: 1696 loop : -0.44 (0.08), residues: 6764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 893 HIS 0.013 0.001 HIS E 26 PHE 0.034 0.001 PHE D3170 TYR 0.033 0.001 TYR B1035 ARG 0.009 0.000 ARG E 50 ********************** 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 856 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 779 time to evaluate : 12.222 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: H 4 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 81 MET cc_start: 0.8286 (tmm) cc_final: 0.7809 (tmm) REVERT: A 399 MET cc_start: 0.7613 (tmm) cc_final: 0.7351 (tmm) REVERT: A 403 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 940 LEU cc_start: 0.9385 (mt) cc_final: 0.9141 (mt) REVERT: A 1165 MET cc_start: 0.8177 (mtp) cc_final: 0.7593 (mtp) REVERT: A 1494 MET cc_start: 0.7807 (tmm) cc_final: 0.7590 (tmm) REVERT: A 1694 MET cc_start: 0.8876 (tpp) cc_final: 0.8655 (tpp) REVERT: A 1948 MET cc_start: 0.7934 (mmp) cc_final: 0.7604 (mmm) REVERT: A 2142 MET cc_start: 0.8380 (tpt) cc_final: 0.8064 (tpp) REVERT: A 2347 MET cc_start: 0.8217 (mmp) cc_final: 0.7824 (mmp) REVERT: A 2493 LEU cc_start: 0.9020 (mm) cc_final: 0.8809 (mp) REVERT: A 2534 LEU cc_start: 0.9187 (mt) cc_final: 0.8830 (tp) REVERT: A 2681 MET cc_start: 0.8529 (tpt) cc_final: 0.7952 (mmm) REVERT: A 2689 MET cc_start: 0.4224 (ptp) cc_final: 0.3672 (ttm) REVERT: A 2695 MET cc_start: 0.5947 (pmm) cc_final: 0.5739 (pmm) REVERT: A 2719 TYR cc_start: 0.8570 (t80) cc_final: 0.8130 (t80) REVERT: A 2828 MET cc_start: 0.7027 (pmm) cc_final: 0.6696 (mtt) REVERT: A 2858 MET cc_start: 0.9023 (mpp) cc_final: 0.8595 (pmm) REVERT: A 2932 TYR cc_start: 0.8461 (t80) cc_final: 0.8028 (t80) REVERT: A 3022 PHE cc_start: 0.8307 (m-10) cc_final: 0.7982 (m-10) REVERT: A 3072 MET cc_start: 0.8985 (mmp) cc_final: 0.8239 (mmm) REVERT: A 3104 MET cc_start: 0.8544 (ppp) cc_final: 0.8191 (ppp) REVERT: A 3159 LEU cc_start: 0.9359 (mm) cc_final: 0.8342 (pp) REVERT: A 3241 MET cc_start: 0.8903 (mtp) cc_final: 0.8690 (mmm) REVERT: A 3981 MET cc_start: 0.8889 (tmm) cc_final: 0.8473 (tmm) REVERT: A 4032 PHE cc_start: 0.8957 (t80) cc_final: 0.8730 (t80) REVERT: A 4048 PHE cc_start: 0.9118 (t80) cc_final: 0.8492 (t80) REVERT: A 4268 MET cc_start: 0.6193 (tmm) cc_final: 0.5899 (tmm) REVERT: A 4274 MET cc_start: 0.5592 (tmm) cc_final: 0.4184 (ptp) REVERT: A 4804 MET cc_start: 0.8759 (mmm) cc_final: 0.8463 (mmm) REVERT: D 81 MET cc_start: 0.8356 (tmm) cc_final: 0.7885 (tmm) REVERT: D 940 LEU cc_start: 0.9334 (mt) cc_final: 0.9076 (mt) REVERT: D 1165 MET cc_start: 0.8301 (mtp) cc_final: 0.7938 (mtp) REVERT: D 1215 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8098 (mtt) REVERT: D 1494 MET cc_start: 0.7785 (tmm) cc_final: 0.7578 (tmm) REVERT: D 2084 MET cc_start: 0.8779 (mtp) cc_final: 0.8565 (mtp) REVERT: D 2142 MET cc_start: 0.8423 (tpt) cc_final: 0.8130 (tpp) REVERT: D 2347 MET cc_start: 0.8515 (mmp) cc_final: 0.8022 (mmp) REVERT: D 2534 LEU cc_start: 0.9062 (mt) cc_final: 0.8655 (tp) REVERT: D 2584 MET cc_start: 0.8646 (mmt) cc_final: 0.8106 (mmm) REVERT: D 2681 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: D 2688 MET cc_start: 0.1172 (ptt) cc_final: 0.0821 (ptt) REVERT: D 2695 MET cc_start: 0.5899 (pmm) cc_final: 0.5654 (pmm) REVERT: D 2719 TYR cc_start: 0.8655 (t80) cc_final: 0.8257 (t80) REVERT: D 2720 PHE cc_start: 0.8613 (t80) cc_final: 0.8104 (t80) REVERT: D 2724 TYR cc_start: 0.8576 (t80) cc_final: 0.8357 (t80) REVERT: D 2782 MET cc_start: 0.8771 (ttp) cc_final: 0.8411 (tmm) REVERT: D 2858 MET cc_start: 0.9150 (mpp) cc_final: 0.8893 (pmm) REVERT: D 2932 TYR cc_start: 0.8599 (t80) cc_final: 0.8195 (t80) REVERT: D 2944 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: D 3072 MET cc_start: 0.8982 (mmm) cc_final: 0.8586 (mmm) REVERT: D 3104 MET cc_start: 0.8539 (ppp) cc_final: 0.8262 (tmm) REVERT: D 3134 LEU cc_start: 0.9266 (mt) cc_final: 0.8968 (mt) REVERT: D 3322 LEU cc_start: 0.8710 (tt) cc_final: 0.8288 (mt) REVERT: D 3323 MET cc_start: 0.8597 (mmm) cc_final: 0.8149 (mmt) REVERT: D 3819 MET cc_start: 0.6638 (ptp) cc_final: 0.6346 (ptp) REVERT: D 4943 MET cc_start: 0.8789 (mtp) cc_final: 0.8312 (mtp) REVERT: B 81 MET cc_start: 0.8196 (tmm) cc_final: 0.7802 (tmm) REVERT: B 241 MET cc_start: 0.5539 (mmp) cc_final: 0.5326 (mmp) REVERT: B 399 MET cc_start: 0.7599 (tmm) cc_final: 0.7277 (tmm) REVERT: B 940 LEU cc_start: 0.9354 (mt) cc_final: 0.9079 (mt) REVERT: B 956 HIS cc_start: 0.9080 (t70) cc_final: 0.8817 (t70) REVERT: B 1035 TYR cc_start: 0.7880 (t80) cc_final: 0.7519 (t80) REVERT: B 1165 MET cc_start: 0.8197 (mtp) cc_final: 0.7808 (mtp) REVERT: B 1168 MET cc_start: 0.8607 (mmm) cc_final: 0.8066 (mmm) REVERT: B 1494 MET cc_start: 0.7772 (tmm) cc_final: 0.7515 (tmm) REVERT: B 1831 MET cc_start: 0.8607 (mtp) cc_final: 0.8245 (mtp) REVERT: B 2066 MET cc_start: 0.8755 (mmp) cc_final: 0.8191 (mmm) REVERT: B 2279 MET cc_start: 0.8616 (ptp) cc_final: 0.8386 (ppp) REVERT: B 2347 MET cc_start: 0.8268 (mmp) cc_final: 0.7796 (mmp) REVERT: B 2384 MET cc_start: 0.8583 (mpp) cc_final: 0.8337 (mpp) REVERT: B 2493 LEU cc_start: 0.9046 (mm) cc_final: 0.8837 (mp) REVERT: B 2719 TYR cc_start: 0.8609 (t80) cc_final: 0.8334 (t80) REVERT: B 2720 PHE cc_start: 0.8619 (t80) cc_final: 0.8256 (t80) REVERT: B 2798 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6710 (mmp) REVERT: B 2840 MET cc_start: 0.8227 (mmm) cc_final: 0.7629 (mmm) REVERT: B 2843 MET cc_start: 0.7881 (ppp) cc_final: 0.7439 (ppp) REVERT: B 2844 MET cc_start: 0.8696 (ppp) cc_final: 0.8367 (ppp) REVERT: B 2858 MET cc_start: 0.8894 (mpp) cc_final: 0.8645 (pmm) REVERT: B 2932 TYR cc_start: 0.8306 (t80) cc_final: 0.7882 (t80) REVERT: B 2944 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: B 3072 MET cc_start: 0.8902 (mmm) cc_final: 0.8504 (mmm) REVERT: B 3109 PHE cc_start: 0.8818 (m-10) cc_final: 0.8536 (m-10) REVERT: B 3241 MET cc_start: 0.8947 (mtp) cc_final: 0.8707 (mtp) REVERT: B 3246 MET cc_start: 0.8546 (tmm) cc_final: 0.8341 (tmm) REVERT: B 3322 LEU cc_start: 0.8522 (tt) cc_final: 0.8098 (mp) REVERT: B 3978 MET cc_start: 0.8981 (ttp) cc_final: 0.8741 (ttt) REVERT: B 4048 PHE cc_start: 0.8718 (m-80) cc_final: 0.8338 (m-80) REVERT: B 4052 MET cc_start: 0.8545 (mtp) cc_final: 0.8058 (ttm) REVERT: B 4256 MET cc_start: 0.8267 (mmt) cc_final: 0.7966 (mmm) REVERT: B 4268 MET cc_start: 0.6393 (tmm) cc_final: 0.6094 (tmm) REVERT: B 4292 MET cc_start: 0.8210 (mmm) cc_final: 0.7894 (mmm) REVERT: B 4943 MET cc_start: 0.8780 (mtp) cc_final: 0.8337 (mtp) REVERT: C 81 MET cc_start: 0.8303 (tmm) cc_final: 0.7910 (tmm) REVERT: C 128 MET cc_start: 0.8606 (mtp) cc_final: 0.8380 (mtp) REVERT: C 241 MET cc_start: 0.5551 (mmp) cc_final: 0.5345 (mmp) REVERT: C 349 MET cc_start: 0.8433 (mmm) cc_final: 0.8175 (mmt) REVERT: C 399 MET cc_start: 0.7560 (tmm) cc_final: 0.7285 (tmm) REVERT: C 956 HIS cc_start: 0.9213 (t70) cc_final: 0.8953 (t70) REVERT: C 1165 MET cc_start: 0.8249 (mtp) cc_final: 0.7718 (mtp) REVERT: C 1494 MET cc_start: 0.7480 (tmm) cc_final: 0.7170 (tmm) REVERT: C 1948 MET cc_start: 0.7994 (mmp) cc_final: 0.7687 (mmm) REVERT: C 2066 MET cc_start: 0.8758 (mmt) cc_final: 0.8405 (mmm) REVERT: C 2279 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (ppp) REVERT: C 2347 MET cc_start: 0.8477 (mmt) cc_final: 0.8063 (mmp) REVERT: C 2384 MET cc_start: 0.8556 (mpp) cc_final: 0.8208 (mpp) REVERT: C 2695 MET cc_start: 0.6075 (pmm) cc_final: 0.5853 (pmm) REVERT: C 2719 TYR cc_start: 0.8614 (t80) cc_final: 0.8263 (t80) REVERT: C 2720 PHE cc_start: 0.8708 (t80) cc_final: 0.8289 (t80) REVERT: C 2840 MET cc_start: 0.9044 (ptm) cc_final: 0.8278 (mmt) REVERT: C 2843 MET cc_start: 0.8098 (ppp) cc_final: 0.7558 (ppp) REVERT: C 2844 MET cc_start: 0.8735 (ppp) cc_final: 0.8507 (ppp) REVERT: C 2858 MET cc_start: 0.9058 (mpp) cc_final: 0.8781 (pmm) REVERT: C 2932 TYR cc_start: 0.8578 (t80) cc_final: 0.8050 (t80) REVERT: C 2944 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: C 3022 PHE cc_start: 0.8387 (m-10) cc_final: 0.7930 (m-10) REVERT: C 3072 MET cc_start: 0.8657 (mmt) cc_final: 0.8301 (mmm) REVERT: C 3159 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8708 (mp) REVERT: C 3263 MET cc_start: 0.8083 (tmm) cc_final: 0.7853 (tpt) REVERT: C 3322 LEU cc_start: 0.8629 (tt) cc_final: 0.8173 (mt) REVERT: C 3323 MET cc_start: 0.8603 (mmp) cc_final: 0.8356 (mmt) REVERT: C 3981 MET cc_start: 0.8894 (tmm) cc_final: 0.8557 (tmm) REVERT: C 4707 MET cc_start: 0.8065 (ttt) cc_final: 0.7849 (ttm) REVERT: C 4748 MET cc_start: 0.7124 (mpp) cc_final: 0.6409 (mpp) REVERT: C 4817 MET cc_start: 0.8591 (mmm) cc_final: 0.8379 (tpt) REVERT: C 4943 MET cc_start: 0.8731 (mtp) cc_final: 0.8344 (mtp) outliers start: 77 outliers final: 61 residues processed: 831 average time/residue: 1.2081 time to fit residues: 1788.3735 Evaluate side-chains 845 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 775 time to evaluate : 12.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2905 ARG Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3821 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 877 HIS Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1306 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2867 ASN Chi-restraints excluded: chain D residue 2944 ASP Chi-restraints excluded: chain D residue 3075 LEU Chi-restraints excluded: chain D residue 3111 HIS Chi-restraints excluded: chain D residue 3821 THR Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 877 HIS Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1306 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2186 GLU Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2771 TYR Chi-restraints excluded: chain B residue 2798 MET Chi-restraints excluded: chain B residue 2944 ASP Chi-restraints excluded: chain B residue 3111 HIS Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2186 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2944 ASP Chi-restraints excluded: chain C residue 3075 LEU Chi-restraints excluded: chain C residue 3111 HIS Chi-restraints excluded: chain C residue 3159 LEU Chi-restraints excluded: chain C residue 3821 THR Chi-restraints excluded: chain C residue 4258 MET Chi-restraints excluded: chain C residue 4752 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 1.9990 chunk 1460 optimal weight: 0.8980 chunk 419 optimal weight: 7.9990 chunk 1264 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 380 optimal weight: 9.9990 chunk 1373 optimal weight: 9.9990 chunk 574 optimal weight: 20.0000 chunk 1409 optimal weight: 0.0970 chunk 173 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3031 ASN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3274 ASN ** C3318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4075 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.047484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.034854 restraints weight = 1611916.413| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.68 r_work: 0.2909 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 141628 Z= 0.157 Angle : 0.616 21.879 191356 Z= 0.303 Chirality : 0.041 0.450 20988 Planarity : 0.004 0.075 24588 Dihedral : 5.143 65.515 19028 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 0.52 % Allowed : 8.45 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.85 (0.07), residues: 17212 helix: 1.50 (0.06), residues: 8736 sheet: -0.10 (0.13), residues: 1704 loop : -0.43 (0.08), residues: 6772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 893 HIS 0.025 0.001 HIS E 26 PHE 0.035 0.001 PHE B3319 TYR 0.034 0.001 TYR B1035 ARG 0.009 0.000 ARG E 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40313.93 seconds wall clock time: 702 minutes 59.84 seconds (42179.84 seconds total)