Starting phenix.real_space_refine on Mon Mar 18 15:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua5_26415/03_2024/7ua5_26415_updated.pdb" } resolution = 2.83 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= 0.013 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88208 2.51 5 N 23596 2.21 5 O 25840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A ARG 1051": "NH1" <-> "NH2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1278": "OD1" <-> "OD2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1623": "OD1" <-> "OD2" Residue "A TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1732": "OE1" <-> "OE2" Residue "A TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2336": "NH1" <-> "NH2" Residue "A GLU 2658": "OE1" <-> "OE2" Residue "A PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2979": "NH1" <-> "NH2" Residue "A PHE 2982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4120": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "H ASP 12": "OD1" <-> "OD2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 810": "OE1" <-> "OE2" Residue "B ARG 1051": "NH1" <-> "NH2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1278": "OD1" <-> "OD2" Residue "B TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1732": "OE1" <-> "OE2" Residue "B TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2336": "NH1" <-> "NH2" Residue "B GLU 2658": "OE1" <-> "OE2" Residue "B PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2979": "NH1" <-> "NH2" Residue "B PHE 2982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4120": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 378": "OD1" <-> "OD2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 810": "OE1" <-> "OE2" Residue "C ARG 1051": "NH1" <-> "NH2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1278": "OD1" <-> "OD2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1623": "OD1" <-> "OD2" Residue "C TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1732": "OE1" <-> "OE2" Residue "C TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2336": "NH1" <-> "NH2" Residue "C GLU 2658": "OE1" <-> "OE2" Residue "C PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2979": "NH1" <-> "NH2" Residue "C PHE 2982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4120": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 810": "OE1" <-> "OE2" Residue "D ARG 1051": "NH1" <-> "NH2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1278": "OD1" <-> "OD2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1623": "OD1" <-> "OD2" Residue "D TYR 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1732": "OE1" <-> "OE2" Residue "D TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2336": "NH1" <-> "NH2" Residue "D GLU 2658": "OE1" <-> "OE2" Residue "D PHE 2895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2979": "NH1" <-> "NH2" Residue "D PHE 2982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4120": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138608 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33092 SG CYS A4888 180.134 204.761 125.857 1.00 74.20 S ATOM 33117 SG CYS A4891 179.126 202.445 122.974 1.00 67.12 S ATOM 70135 SG CYS B4888 203.952 195.619 125.894 1.00 74.31 S ATOM 70160 SG CYS B4891 201.640 196.628 123.009 1.00 68.62 S ATOM A030I SG CYS C4888 194.789 171.756 125.805 1.00 73.49 S ATOM A0317 SG CYS C4891 195.793 174.071 122.920 1.00 68.89 S ATOM A0T2L SG CYS D4888 171.137 180.620 126.024 1.00 76.62 S ATOM A0T3A SG CYS D4891 173.454 179.603 123.145 1.00 69.81 S Time building chain proxies: 93.36, per 1000 atoms: 0.67 Number of scatterers: 138608 At special positions: 0 Unit cell: (375.813, 376.65, 213.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 936 16.00 P 24 15.00 O 25840 8.00 N 23596 7.00 C 88208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.22 Conformation dependent library (CDL) restraints added in 33.2 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: 692 helices and 80 sheets defined 59.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 41.89 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.091A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.521A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.755A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.842A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.198A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.600A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.598A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.797A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.459A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.886A 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 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.626A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.668A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.606A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.452A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.841A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.853A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.108A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.420A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.888A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.389A 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: 7.046A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.934A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.052A 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: 3.769A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.373A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.778A 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: 3.612A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.802A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.832A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.577A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.554A pdb=" N SER A1803 " --> pdb=" O VAL A1799 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.273A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 4.244A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1967 removed outlier: 4.451A pdb=" N THR A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1959 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 4.179A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.673A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.565A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.767A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.914A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.347A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 removed outlier: 3.601A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 5.367A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.514A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.981A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.666A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 removed outlier: 3.695A pdb=" N GLY A2284 " --> pdb=" O LEU A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.603A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.023A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 3.620A pdb=" N ILE A2436 " --> pdb=" O LEU A2432 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.770A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.670A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 3.854A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.939A 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: 5.177A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 5.389A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2586 removed outlier: 4.389A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2581 through 2586' Processing helix chain 'A' and resid 2587 through 2597 removed outlier: 3.871A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) Proline residue: A2597 - end of helix Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.902A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.125A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 3.710A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.521A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS A2723 " --> pdb=" O TYR A2719 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A2724 " --> pdb=" O PHE A2720 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU A2726 " --> pdb=" O ASN A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.565A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2785 removed outlier: 5.433A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.814A pdb=" N TRP A2785 " --> pdb=" O THR A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.009A pdb=" N MET A2798 " --> pdb=" O GLU A2794 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A2799 " --> pdb=" O GLY A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.464A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.655A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2921 removed outlier: 4.400A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A2921 " --> pdb=" O ILE A2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2916 through 2921' Processing helix chain 'A' and resid 2922 through 2948 removed outlier: 4.237A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.541A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2980 through 2985 removed outlier: 4.771A pdb=" N ALA A2985 " --> pdb=" O TYR A2981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3018 removed outlier: 5.671A pdb=" N HIS A3017 " --> pdb=" O VAL A3013 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A3018 " --> pdb=" O LEU A3014 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3049 removed outlier: 3.638A pdb=" N GLY A3049 " --> pdb=" O VAL A3045 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3078 Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.706A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3118 through 3124 removed outlier: 4.274A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU A3124 " --> pdb=" O ASP A3120 " (cutoff:3.500A) Processing helix chain 'A' and resid 3125 through 3143 removed outlier: 4.137A pdb=" N SER A3129 " --> pdb=" O ASP A3125 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3166 removed outlier: 4.168A pdb=" N LEU A3159 " --> pdb=" O LEU A3155 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A3160 " --> pdb=" O GLY A3156 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 3.677A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3180' Processing helix chain 'A' and resid 3182 through 3188 removed outlier: 4.188A pdb=" N SER A3188 " --> pdb=" O TYR A3184 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.603A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 4.300A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 4.910A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 removed outlier: 3.947A pdb=" N ASN A3257 " --> pdb=" O GLY A3253 " (cutoff:3.500A) Proline residue: A3258 - end of helix No H-bonds generated for 'chain 'A' and resid 3253 through 3258' Processing helix chain 'A' and resid 3269 through 3291 removed outlier: 3.950A pdb=" N GLY A3278 " --> pdb=" O ASN A3274 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.497A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 3.919A pdb=" N ASN A3308 " --> pdb=" O GLN A3304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3330 removed outlier: 6.636A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 4.197A pdb=" N ALA A3330 " --> pdb=" O LEU A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 4.369A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.787A 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 3628 Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 3.531A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 5.033A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.720A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 4.106A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.820A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.947A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.645A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.967A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.680A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.597A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.730A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.661A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.644A pdb=" N LYS A3976 " --> pdb=" O MET A3972 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.565A pdb=" N LYS A4022 " --> pdb=" O ASP A4018 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.871A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.041A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 Proline residue: A4090 - end of helix removed outlier: 3.754A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 removed outlier: 5.215A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4261 removed outlier: 3.767A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4272 removed outlier: 4.028A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.793A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.623A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.232A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.117A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 4.064A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 6.076A 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: 3.887A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.781A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.733A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.402A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.510A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.327A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.939A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 3.842A 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 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.254A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.091A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.520A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.755A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.843A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.197A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.600A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 3.598A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.797A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.459A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.887A 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 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.626A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.668A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.606A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.452A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.841A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.852A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 4.108A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.420A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.887A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.389A 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: 7.047A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1230 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.934A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.051A 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: 3.769A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.373A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.778A 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: 3.613A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.802A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.832A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.577A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.554A pdb=" N SER B1803 " --> pdb=" O VAL B1799 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.272A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 4.244A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1967 removed outlier: 4.452A pdb=" N THR B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1959 " --> pdb=" O ALA B1955 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 4.179A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.674A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.566A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.765A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.914A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.347A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 removed outlier: 3.601A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 5.368A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.514A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.981A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.667A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 removed outlier: 3.695A pdb=" N GLY B2284 " --> pdb=" O LEU B2280 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.603A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B2320 " --> pdb=" O ASN B2316 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.023A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B2409 " --> pdb=" O GLU B2405 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 3.621A pdb=" N ILE B2436 " --> pdb=" O LEU B2432 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.770A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.670A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 3.854A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.938A 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: 5.176A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 5.390A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2586 removed outlier: 4.390A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2581 through 2586' Processing helix chain 'B' and resid 2587 through 2597 removed outlier: 3.873A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) Proline residue: B2597 - end of helix Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.901A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.125A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 3.710A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.521A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS B2723 " --> pdb=" O TYR B2719 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR B2724 " --> pdb=" O PHE B2720 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU B2726 " --> pdb=" O ASN B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.566A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2785 removed outlier: 5.433A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP B2773 " --> pdb=" O GLU B2769 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.815A pdb=" N TRP B2785 " --> pdb=" O THR B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.009A pdb=" N MET B2798 " --> pdb=" O GLU B2794 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B2799 " --> pdb=" O GLY B2795 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.464A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.656A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2921 removed outlier: 4.400A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE B2921 " --> pdb=" O ILE B2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2916 through 2921' Processing helix chain 'B' and resid 2922 through 2948 removed outlier: 4.237A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.541A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2980 through 2985 removed outlier: 4.770A pdb=" N ALA B2985 " --> pdb=" O TYR B2981 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3018 removed outlier: 5.671A pdb=" N HIS B3017 " --> pdb=" O VAL B3013 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B3018 " --> pdb=" O LEU B3014 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3049 removed outlier: 3.638A pdb=" N GLY B3049 " --> pdb=" O VAL B3045 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3078 Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.705A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3118 through 3124 removed outlier: 4.273A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU B3124 " --> pdb=" O ASP B3120 " (cutoff:3.500A) Processing helix chain 'B' and resid 3125 through 3143 removed outlier: 4.138A pdb=" N SER B3129 " --> pdb=" O ASP B3125 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3166 removed outlier: 4.168A pdb=" N LEU B3159 " --> pdb=" O LEU B3155 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B3160 " --> pdb=" O GLY B3156 " (cutoff:3.500A) Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 3.678A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3180' Processing helix chain 'B' and resid 3182 through 3188 removed outlier: 4.188A pdb=" N SER B3188 " --> pdb=" O TYR B3184 " (cutoff:3.500A) Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.603A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 4.301A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 4.910A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 removed outlier: 3.947A pdb=" N ASN B3257 " --> pdb=" O GLY B3253 " (cutoff:3.500A) Proline residue: B3258 - end of helix No H-bonds generated for 'chain 'B' and resid 3253 through 3258' Processing helix chain 'B' and resid 3269 through 3291 removed outlier: 3.950A pdb=" N GLY B3278 " --> pdb=" O ASN B3274 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.497A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 3.918A pdb=" N ASN B3308 " --> pdb=" O GLN B3304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3330 removed outlier: 6.637A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 4.197A pdb=" N ALA B3330 " --> pdb=" O LEU B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 4.369A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.787A 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 3628 Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 3.531A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 5.032A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.721A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 4.107A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.819A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.947A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.645A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.968A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.680A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.598A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.730A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.662A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.643A pdb=" N LYS B3976 " --> pdb=" O MET B3972 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.565A pdb=" N LYS B4022 " --> pdb=" O ASP B4018 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.872A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.041A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 Proline residue: B4090 - end of helix removed outlier: 3.754A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 removed outlier: 5.215A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4261 removed outlier: 3.766A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4272 removed outlier: 4.028A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.793A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.623A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.232A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.116A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 4.064A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 6.075A 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: 3.887A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.780A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.733A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.401A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.510A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.328A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.939A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 3.842A 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 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.254A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.091A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.521A pdb=" N ALA C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 224' Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.755A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.843A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.197A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.600A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.599A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.797A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.459A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.886A 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 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.627A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.668A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.607A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.453A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.379A 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: 4.841A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.853A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 961 removed outlier: 4.108A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.420A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.887A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.389A 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: 7.046A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1230 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.933A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.051A 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: 3.769A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.374A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.777A 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: 3.613A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.803A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.832A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.577A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.554A pdb=" N SER C1803 " --> pdb=" O VAL C1799 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.272A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 4.245A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1967 removed outlier: 4.452A pdb=" N THR C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C1959 " --> pdb=" O ALA C1955 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 4.179A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.674A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.566A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.766A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.915A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.347A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 removed outlier: 3.600A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 5.367A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.513A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.982A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.666A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 removed outlier: 3.695A pdb=" N GLY C2284 " --> pdb=" O LEU C2280 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.601A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C2320 " --> pdb=" O ASN C2316 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.022A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C2409 " --> pdb=" O GLU C2405 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 3.620A pdb=" N ILE C2436 " --> pdb=" O LEU C2432 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.770A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.669A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 3.854A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.937A 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: 5.178A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 5.389A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2586 removed outlier: 4.390A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2581 through 2586' Processing helix chain 'C' and resid 2587 through 2597 removed outlier: 3.872A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) Proline residue: C2597 - end of helix Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.902A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.125A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 3.711A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.522A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS C2723 " --> pdb=" O TYR C2719 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR C2724 " --> pdb=" O PHE C2720 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU C2726 " --> pdb=" O ASN C2722 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.565A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2785 removed outlier: 5.432A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP C2773 " --> pdb=" O GLU C2769 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.815A pdb=" N TRP C2785 " --> pdb=" O THR C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.009A pdb=" N MET C2798 " --> pdb=" O GLU C2794 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA C2799 " --> pdb=" O GLY C2795 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.465A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.655A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2921 removed outlier: 4.400A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE C2921 " --> pdb=" O ILE C2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2916 through 2921' Processing helix chain 'C' and resid 2922 through 2948 removed outlier: 4.237A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.541A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2980 through 2985 removed outlier: 4.771A pdb=" N ALA C2985 " --> pdb=" O TYR C2981 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3018 removed outlier: 5.669A pdb=" N HIS C3017 " --> pdb=" O VAL C3013 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG C3018 " --> pdb=" O LEU C3014 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3049 removed outlier: 3.638A pdb=" N GLY C3049 " --> pdb=" O VAL C3045 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3078 Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.705A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3118 through 3124 removed outlier: 4.273A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU C3124 " --> pdb=" O ASP C3120 " (cutoff:3.500A) Processing helix chain 'C' and resid 3125 through 3143 removed outlier: 4.137A pdb=" N SER C3129 " --> pdb=" O ASP C3125 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3166 removed outlier: 4.168A pdb=" N LEU C3159 " --> pdb=" O LEU C3155 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA C3160 " --> pdb=" O GLY C3156 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 3.678A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3180' Processing helix chain 'C' and resid 3182 through 3188 removed outlier: 4.187A pdb=" N SER C3188 " --> pdb=" O TYR C3184 " (cutoff:3.500A) Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.602A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 4.301A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 4.910A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 removed outlier: 3.948A pdb=" N ASN C3257 " --> pdb=" O GLY C3253 " (cutoff:3.500A) Proline residue: C3258 - end of helix No H-bonds generated for 'chain 'C' and resid 3253 through 3258' Processing helix chain 'C' and resid 3269 through 3291 removed outlier: 3.950A pdb=" N GLY C3278 " --> pdb=" O ASN C3274 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.497A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 3.919A pdb=" N ASN C3308 " --> pdb=" O GLN C3304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3330 removed outlier: 6.636A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 4.198A pdb=" N ALA C3330 " --> pdb=" O LEU C3326 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 4.369A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.787A 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 3628 Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 3.530A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 5.033A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.720A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 4.106A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.819A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.946A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.646A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.968A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.680A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.597A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.730A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.662A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.643A pdb=" N LYS C3976 " --> pdb=" O MET C3972 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.565A pdb=" N LYS C4022 " --> pdb=" O ASP C4018 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.871A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.040A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 Proline residue: C4090 - end of helix removed outlier: 3.754A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 removed outlier: 5.215A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4261 removed outlier: 3.767A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4272 removed outlier: 4.028A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.793A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.623A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.231A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.117A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 4.064A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 6.076A 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: 3.888A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.780A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.733A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.402A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.509A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.327A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.940A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 3.842A 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 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.254A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.091A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.521A pdb=" N ALA D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 224' Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.755A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.843A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.197A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.599A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 3.599A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.796A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.459A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.887A 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 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.627A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.668A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.606A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.452A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.841A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 3.852A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 961 removed outlier: 4.107A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.420A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.887A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.390A 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: 7.047A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1230 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.934A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.051A 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: 3.770A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.374A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.777A 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: 3.612A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.803A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.832A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.577A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.554A pdb=" N SER D1803 " --> pdb=" O VAL D1799 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.272A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 4.244A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1967 removed outlier: 4.451A pdb=" N THR D1958 " --> pdb=" O SER D1954 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D1959 " --> pdb=" O ALA D1955 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 4.179A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.674A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.565A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.765A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.914A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.346A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 removed outlier: 3.601A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 5.368A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.513A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.981A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.666A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 removed outlier: 3.695A pdb=" N GLY D2284 " --> pdb=" O LEU D2280 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.603A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D2320 " --> pdb=" O ASN D2316 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.022A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D2409 " --> pdb=" O GLU D2405 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 3.620A pdb=" N ILE D2436 " --> pdb=" O LEU D2432 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.770A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.670A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 3.855A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.938A 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: 5.178A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 5.389A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2586 removed outlier: 4.390A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2581 through 2586' Processing helix chain 'D' and resid 2587 through 2597 removed outlier: 3.871A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) Proline residue: D2597 - end of helix Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.902A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.125A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 3.711A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.521A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS D2723 " --> pdb=" O TYR D2719 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D2724 " --> pdb=" O PHE D2720 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU D2726 " --> pdb=" O ASN D2722 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.566A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2785 removed outlier: 5.433A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP D2773 " --> pdb=" O GLU D2769 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.815A pdb=" N TRP D2785 " --> pdb=" O THR D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.009A pdb=" N MET D2798 " --> pdb=" O GLU D2794 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D2799 " --> pdb=" O GLY D2795 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.465A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.655A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2921 removed outlier: 4.400A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE D2921 " --> pdb=" O ILE D2917 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2916 through 2921' Processing helix chain 'D' and resid 2922 through 2948 removed outlier: 4.236A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.541A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2980 through 2985 removed outlier: 4.769A pdb=" N ALA D2985 " --> pdb=" O TYR D2981 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3018 removed outlier: 5.671A pdb=" N HIS D3017 " --> pdb=" O VAL D3013 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D3018 " --> pdb=" O LEU D3014 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3049 removed outlier: 3.638A pdb=" N GLY D3049 " --> pdb=" O VAL D3045 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3078 Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.705A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3118 through 3124 removed outlier: 4.274A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU D3124 " --> pdb=" O ASP D3120 " (cutoff:3.500A) Processing helix chain 'D' and resid 3125 through 3143 removed outlier: 4.136A pdb=" N SER D3129 " --> pdb=" O ASP D3125 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3166 removed outlier: 4.167A pdb=" N LEU D3159 " --> pdb=" O LEU D3155 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA D3160 " --> pdb=" O GLY D3156 " (cutoff:3.500A) Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 3.677A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3180' Processing helix chain 'D' and resid 3182 through 3188 removed outlier: 4.187A pdb=" N SER D3188 " --> pdb=" O TYR D3184 " (cutoff:3.500A) Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.602A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 4.301A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 4.910A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 removed outlier: 3.948A pdb=" N ASN D3257 " --> pdb=" O GLY D3253 " (cutoff:3.500A) Proline residue: D3258 - end of helix No H-bonds generated for 'chain 'D' and resid 3253 through 3258' Processing helix chain 'D' and resid 3269 through 3291 removed outlier: 3.950A pdb=" N GLY D3278 " --> pdb=" O ASN D3274 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.497A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 3.919A pdb=" N ASN D3308 " --> pdb=" O GLN D3304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3330 removed outlier: 6.637A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 4.197A pdb=" N ALA D3330 " --> pdb=" O LEU D3326 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 4.369A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.786A 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 3628 Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 3.531A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 5.033A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.720A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 4.107A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.819A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.947A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.645A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.967A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.680A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.598A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.730A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.661A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.644A pdb=" N LYS D3976 " --> pdb=" O MET D3972 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.566A pdb=" N LYS D4022 " --> pdb=" O ASP D4018 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.871A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.041A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 Proline residue: D4090 - end of helix removed outlier: 3.754A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 removed outlier: 5.214A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4261 removed outlier: 3.767A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4272 removed outlier: 4.028A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.793A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.623A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.232A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.117A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 4.064A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 6.076A 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: 3.888A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.780A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.733A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.401A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.509A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.328A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.939A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 3.842A 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 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.255A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.779A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.244A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.749A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.779A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.243A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.750A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.779A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.244A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.750A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.779A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.243A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.749A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.105A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.258A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.605A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 160 through 165 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 5, first strand: chain 'A' and resid 295 through 299 removed outlier: 4.087A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.774A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.830A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.719A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.361A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 3.530A pdb=" N GLY A1019 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 7.383A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.655A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.825A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 3.645A pdb=" N ILE A2742 " --> pdb=" O LYS A2752 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 18, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.673A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 20, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.105A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.258A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.606A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 160 through 165 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 24, first strand: chain 'B' and resid 295 through 299 removed outlier: 4.087A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 26, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 27, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.774A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.829A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.719A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.361A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 3.530A pdb=" N GLY B1019 " --> pdb=" O ASN B1029 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 7.383A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.655A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.825A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 3.646A pdb=" N ILE B2742 " --> pdb=" O LYS B2752 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 37, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.672A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 39, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.106A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.259A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.606A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 160 through 165 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 43, first strand: chain 'C' and resid 295 through 299 removed outlier: 4.088A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 45, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 46, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.775A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.829A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.718A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.362A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 3.530A pdb=" N GLY C1019 " --> pdb=" O ASN C1029 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 7.383A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.655A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.825A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 3.646A pdb=" N ILE C2742 " --> pdb=" O LYS C2752 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 56, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.673A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 58, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.105A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.257A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.606A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 160 through 165 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 62, first strand: chain 'D' and resid 295 through 299 removed outlier: 4.087A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 64, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 65, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.775A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.829A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.718A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.361A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 3.530A pdb=" N GLY D1019 " --> pdb=" O ASN D1029 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 7.383A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.655A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.825A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 3.645A pdb=" N ILE D2742 " --> pdb=" O LYS D2752 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 75, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.673A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 77, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.643A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.644A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.644A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.643A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 7284 hydrogen bonds defined for protein. 21736 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: 100.88 Time building geometry restraints manager: 45.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 44708 1.34 - 1.46: 32142 1.46 - 1.59: 63234 1.59 - 1.71: 32 1.71 - 1.83: 1512 Bond restraints: 141628 Sorted by residual: bond pdb=" CG LYS A2856 " pdb=" CD LYS A2856 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.50e+00 bond pdb=" CG LYS B2856 " pdb=" CD LYS B2856 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.49e+00 bond pdb=" CG LYS D2856 " pdb=" CD LYS D2856 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.41e+00 bond pdb=" CG LYS C2856 " pdb=" CD LYS C2856 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.39e+00 bond pdb=" CG LEU D2763 " pdb=" CD1 LEU D2763 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.59e+00 ... (remaining 141623 not shown) Histogram of bond angle deviations from ideal: 96.85 - 106.00: 3195 106.00 - 115.15: 85120 115.15 - 124.31: 100157 124.31 - 133.46: 2652 133.46 - 142.62: 232 Bond angle restraints: 191356 Sorted by residual: angle pdb=" CA LEU C3315 " pdb=" CB LEU C3315 " pdb=" CG LEU C3315 " ideal model delta sigma weight residual 116.30 142.62 -26.32 3.50e+00 8.16e-02 5.65e+01 angle pdb=" CA LEU B3315 " pdb=" CB LEU B3315 " pdb=" CG LEU B3315 " ideal model delta sigma weight residual 116.30 142.61 -26.31 3.50e+00 8.16e-02 5.65e+01 angle pdb=" CA LEU A3315 " pdb=" CB LEU A3315 " pdb=" CG LEU A3315 " ideal model delta sigma weight residual 116.30 142.60 -26.30 3.50e+00 8.16e-02 5.65e+01 angle pdb=" CA LEU D3315 " pdb=" CB LEU D3315 " pdb=" CG LEU D3315 " ideal model delta sigma weight residual 116.30 142.59 -26.29 3.50e+00 8.16e-02 5.64e+01 angle pdb=" CB MET D2840 " pdb=" CG MET D2840 " pdb=" SD MET D2840 " ideal model delta sigma weight residual 112.70 132.72 -20.02 3.00e+00 1.11e-01 4.45e+01 ... (remaining 191351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 76815 17.89 - 35.78: 6842 35.78 - 53.67: 1101 53.67 - 71.56: 499 71.56 - 89.45: 155 Dihedral angle restraints: 85412 sinusoidal: 35052 harmonic: 50360 Sorted by residual: dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual -180.00 -138.47 -41.53 0 5.00e+00 4.00e-02 6.90e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -138.47 -41.53 0 5.00e+00 4.00e-02 6.90e+01 dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual 180.00 -138.49 -41.51 0 5.00e+00 4.00e-02 6.89e+01 ... (remaining 85409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 18912 0.071 - 0.142: 1982 0.142 - 0.212: 74 0.212 - 0.283: 16 0.283 - 0.354: 4 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CG LEU B3276 " pdb=" CB LEU B3276 " pdb=" CD1 LEU B3276 " pdb=" CD2 LEU B3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CG LEU D3276 " pdb=" CB LEU D3276 " pdb=" CD1 LEU D3276 " pdb=" CD2 LEU D3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CG LEU C3276 " pdb=" CB LEU C3276 " pdb=" CD1 LEU C3276 " pdb=" CD2 LEU C3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1051 " 0.853 9.50e-02 1.11e+02 3.82e-01 8.87e+01 pdb=" NE ARG C1051 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG C1051 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C1051 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C1051 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1051 " 0.853 9.50e-02 1.11e+02 3.82e-01 8.87e+01 pdb=" NE ARG A1051 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A1051 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A1051 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1051 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1051 " 0.853 9.50e-02 1.11e+02 3.82e-01 8.86e+01 pdb=" NE ARG D1051 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D1051 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D1051 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D1051 " 0.022 2.00e-02 2.50e+03 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 707 2.51 - 3.11: 101989 3.11 - 3.70: 221871 3.70 - 4.30: 319355 4.30 - 4.90: 518311 Nonbonded interactions: 1162233 Sorted by model distance: nonbonded pdb=" NE2 GLN A1498 " pdb=" O ASN D2899 " model vdw 1.909 2.520 nonbonded pdb=" NH2 ARG A 882 " pdb=" O LEU A 933 " model vdw 1.922 2.520 nonbonded pdb=" NH2 ARG C 882 " pdb=" O LEU C 933 " model vdw 1.923 2.520 nonbonded pdb=" NH2 ARG D 882 " pdb=" O LEU D 933 " model vdw 1.923 2.520 nonbonded pdb=" NH2 ARG B 882 " pdb=" O LEU B 933 " model vdw 1.923 2.520 ... (remaining 1162228 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: 9.350 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: 0.110 Extract box with map and model: 30.880 Check model and map are aligned: 1.460 Set scattering table: 0.940 Process input model: 434.770 Find NCS groups from input model: 7.000 Set up NCS constraints: 0.950 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: 0.030 Load rotamer database and sin/cos tables:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 494.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.082 141628 Z= 0.214 Angle : 0.779 26.316 191356 Z= 0.433 Chirality : 0.043 0.354 20988 Planarity : 0.008 0.382 24588 Dihedral : 14.816 89.446 52936 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 1.41 % Allowed : 1.11 % Favored : 97.48 % 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: 0.85 (0.06), residues: 17212 helix: 1.42 (0.06), residues: 8868 sheet: 0.37 (0.13), residues: 1692 loop : -0.48 (0.07), residues: 6652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B2732 HIS 0.018 0.001 HIS B3178 PHE 0.067 0.002 PHE A2662 TYR 0.032 0.002 TYR C3245 ARG 0.035 0.001 ARG H 14 *********************** 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 1245 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1033 time to evaluate : 11.519 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: A 930 ASN cc_start: 0.8932 (m110) cc_final: 0.8542 (m-40) REVERT: A 940 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8602 (pp) REVERT: A 995 MET cc_start: 0.8186 (mtm) cc_final: 0.7825 (ttt) REVERT: A 2279 MET cc_start: 0.8305 (tmm) cc_final: 0.7965 (tmm) REVERT: A 2695 MET cc_start: 0.4692 (OUTLIER) cc_final: 0.4487 (mmm) REVERT: A 2722 ASN cc_start: 0.9561 (m-40) cc_final: 0.8986 (m110) REVERT: A 2723 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8678 (mptt) REVERT: A 2724 TYR cc_start: 0.9056 (t80) cc_final: 0.8585 (t80) REVERT: A 2757 MET cc_start: 0.7748 (mtt) cc_final: 0.7064 (mpt) REVERT: A 2837 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9163 (tt) REVERT: A 2843 MET cc_start: 0.8003 (tpt) cc_final: 0.7356 (tpt) REVERT: A 2844 MET cc_start: 0.8811 (ppp) cc_final: 0.8557 (ppp) REVERT: A 2847 ASN cc_start: 0.8727 (t0) cc_final: 0.8394 (t0) REVERT: A 2877 LEU cc_start: 0.8842 (mt) cc_final: 0.8517 (mt) REVERT: A 2880 LYS cc_start: 0.9275 (mppt) cc_final: 0.8970 (mppt) REVERT: A 2893 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 2895 PHE cc_start: 0.9262 (t80) cc_final: 0.8843 (t80) REVERT: A 2899 ASN cc_start: 0.8800 (m-40) cc_final: 0.8128 (m110) REVERT: A 2980 LEU cc_start: 0.8686 (tt) cc_final: 0.8478 (tm) REVERT: A 3007 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8751 (mt) REVERT: A 3014 LEU cc_start: 0.8796 (mm) cc_final: 0.8594 (mm) REVERT: A 3104 MET cc_start: 0.8640 (ptt) cc_final: 0.8433 (ptt) REVERT: A 3116 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8803 (tp-100) REVERT: A 3131 TYR cc_start: 0.9233 (m-10) cc_final: 0.8910 (m-80) REVERT: A 3162 PHE cc_start: 0.8830 (t80) cc_final: 0.8629 (t80) REVERT: A 3249 TRP cc_start: 0.7025 (m-90) cc_final: 0.6721 (m-90) REVERT: A 3252 HIS cc_start: 0.8349 (m90) cc_final: 0.8041 (m-70) REVERT: A 3296 MET cc_start: 0.9178 (ptp) cc_final: 0.8774 (ptt) REVERT: A 4306 PHE cc_start: 0.7433 (m-80) cc_final: 0.7160 (m-10) REVERT: B 930 ASN cc_start: 0.8903 (m110) cc_final: 0.8462 (m-40) REVERT: B 940 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8634 (pp) REVERT: B 995 MET cc_start: 0.8511 (mtm) cc_final: 0.8093 (ttp) REVERT: B 1050 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9015 (tp) REVERT: B 2592 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 2719 TYR cc_start: 0.8250 (t80) cc_final: 0.7841 (t80) REVERT: B 2724 TYR cc_start: 0.8815 (t80) cc_final: 0.8361 (t80) REVERT: B 2757 MET cc_start: 0.7737 (mtt) cc_final: 0.7154 (mpt) REVERT: B 2828 MET cc_start: 0.8217 (mmp) cc_final: 0.7844 (mpp) REVERT: B 2837 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9201 (tm) REVERT: B 2840 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7343 (mmt) REVERT: B 2843 MET cc_start: 0.8002 (tpt) cc_final: 0.7350 (tpt) REVERT: B 2844 MET cc_start: 0.8774 (ppp) cc_final: 0.8478 (ppp) REVERT: B 2895 PHE cc_start: 0.9261 (t80) cc_final: 0.8861 (t80) REVERT: B 2899 ASN cc_start: 0.8755 (m-40) cc_final: 0.8127 (m110) REVERT: B 2939 TYR cc_start: 0.8420 (m-80) cc_final: 0.8213 (m-80) REVERT: B 2963 PHE cc_start: 0.8236 (t80) cc_final: 0.7974 (t80) REVERT: B 3252 HIS cc_start: 0.8282 (m90) cc_final: 0.7961 (m-70) REVERT: B 3296 MET cc_start: 0.9216 (ptp) cc_final: 0.8563 (ptp) REVERT: B 4048 PHE cc_start: 0.8655 (t80) cc_final: 0.8365 (t80) REVERT: B 4306 PHE cc_start: 0.7589 (m-80) cc_final: 0.7291 (m-10) REVERT: C 940 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 995 MET cc_start: 0.8069 (mtm) cc_final: 0.7609 (ttt) REVERT: C 1975 MET cc_start: 0.8181 (ppp) cc_final: 0.7935 (ppp) REVERT: C 2279 MET cc_start: 0.8186 (tmm) cc_final: 0.7800 (tmm) REVERT: C 2695 MET cc_start: 0.3836 (OUTLIER) cc_final: 0.3598 (mmm) REVERT: C 2723 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9010 (mptt) REVERT: C 2724 TYR cc_start: 0.8868 (t80) cc_final: 0.8437 (t80) REVERT: C 2757 MET cc_start: 0.7611 (mtt) cc_final: 0.6935 (mpt) REVERT: C 2782 MET cc_start: 0.8058 (ptm) cc_final: 0.7578 (ppp) REVERT: C 2843 MET cc_start: 0.7643 (tpt) cc_final: 0.6985 (tpt) REVERT: C 2844 MET cc_start: 0.8687 (ppp) cc_final: 0.8410 (ppp) REVERT: C 2877 LEU cc_start: 0.8795 (mt) cc_final: 0.8401 (mt) REVERT: C 2895 PHE cc_start: 0.9170 (t80) cc_final: 0.8750 (t80) REVERT: C 2899 ASN cc_start: 0.8408 (m-40) cc_final: 0.7643 (m110) REVERT: C 2963 PHE cc_start: 0.8141 (t80) cc_final: 0.7818 (t80) REVERT: C 2975 PHE cc_start: 0.8647 (m-80) cc_final: 0.8383 (m-10) REVERT: C 3014 LEU cc_start: 0.8849 (mm) cc_final: 0.8633 (mm) REVERT: C 3033 LEU cc_start: 0.8949 (mt) cc_final: 0.8735 (mt) REVERT: C 3101 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7545 (mp) REVERT: C 3104 MET cc_start: 0.8544 (ptt) cc_final: 0.7700 (pp-130) REVERT: C 3108 LEU cc_start: 0.9237 (mt) cc_final: 0.8988 (mt) REVERT: C 3111 HIS cc_start: 0.8191 (p-80) cc_final: 0.7672 (p-80) REVERT: C 3116 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8863 (tp-100) REVERT: C 3249 TRP cc_start: 0.7180 (m-90) cc_final: 0.6636 (m-90) REVERT: C 3252 HIS cc_start: 0.8426 (m90) cc_final: 0.8072 (m-70) REVERT: C 3295 TRP cc_start: 0.8492 (p-90) cc_final: 0.8222 (p-90) REVERT: C 3296 MET cc_start: 0.9260 (ptp) cc_final: 0.9011 (ptp) REVERT: D 309 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: D 317 MET cc_start: 0.7141 (ptm) cc_final: 0.6892 (ptm) REVERT: D 940 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8953 (pp) REVERT: D 946 LEU cc_start: 0.9070 (mt) cc_final: 0.8793 (pp) REVERT: D 995 MET cc_start: 0.8675 (mtm) cc_final: 0.8447 (mtt) REVERT: D 999 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9079 (mt) REVERT: D 1050 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9073 (tt) REVERT: D 1721 MET cc_start: 0.7576 (mmt) cc_final: 0.7310 (mpp) REVERT: D 2279 MET cc_start: 0.8359 (tmm) cc_final: 0.8156 (tmm) REVERT: D 2561 LEU cc_start: 0.8343 (mp) cc_final: 0.8140 (mt) REVERT: D 2681 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: D 2724 TYR cc_start: 0.9018 (t80) cc_final: 0.8559 (t80) REVERT: D 2757 MET cc_start: 0.7650 (mtt) cc_final: 0.6874 (mpt) REVERT: D 2782 MET cc_start: 0.7922 (ptm) cc_final: 0.7621 (ptt) REVERT: D 2785 TRP cc_start: 0.8195 (m-10) cc_final: 0.6763 (m-10) REVERT: D 2840 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8038 (tpp) REVERT: D 2843 MET cc_start: 0.8583 (tpt) cc_final: 0.7700 (tpt) REVERT: D 2880 LYS cc_start: 0.9188 (mppt) cc_final: 0.8847 (mppt) REVERT: D 2893 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8490 (mm) REVERT: D 2898 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8829 (pt) REVERT: D 2899 ASN cc_start: 0.9046 (m-40) cc_final: 0.8340 (m110) REVERT: D 2980 LEU cc_start: 0.8723 (tt) cc_final: 0.8439 (tm) REVERT: D 3003 MET cc_start: 0.8405 (mtm) cc_final: 0.8157 (mtp) REVERT: D 3007 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (mt) REVERT: D 3104 MET cc_start: 0.8603 (ptt) cc_final: 0.8355 (ptt) REVERT: D 3131 TYR cc_start: 0.8857 (m-10) cc_final: 0.8527 (m-80) REVERT: D 3162 PHE cc_start: 0.8669 (t80) cc_final: 0.8416 (t80) REVERT: D 3231 MET cc_start: 0.9214 (tpt) cc_final: 0.8927 (tpp) REVERT: D 3252 HIS cc_start: 0.7812 (m90) cc_final: 0.7554 (m-70) REVERT: D 3296 MET cc_start: 0.9105 (ptp) cc_final: 0.8586 (ptt) REVERT: D 4048 PHE cc_start: 0.8341 (t80) cc_final: 0.8034 (t80) REVERT: D 4305 PHE cc_start: 0.7875 (t80) cc_final: 0.7643 (t80) REVERT: D 4306 PHE cc_start: 0.7408 (m-80) cc_final: 0.7111 (m-10) outliers start: 212 outliers final: 15 residues processed: 1121 average time/residue: 1.9805 time to fit residues: 3216.7378 Evaluate side-chains 940 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 901 time to evaluate : 11.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2837 LEU Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 3007 LEU Chi-restraints excluded: chain A residue 3116 GLN Chi-restraints excluded: chain A residue 4264 LEU Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2592 LEU Chi-restraints excluded: chain B residue 2607 LEU Chi-restraints excluded: chain B residue 2727 HIS Chi-restraints excluded: chain B residue 2837 LEU Chi-restraints excluded: chain B residue 2840 MET Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2727 HIS Chi-restraints excluded: chain C residue 2731 LYS Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3116 GLN Chi-restraints excluded: chain C residue 4264 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 2681 MET Chi-restraints excluded: chain D residue 2727 HIS Chi-restraints excluded: chain D residue 2840 MET Chi-restraints excluded: chain D residue 2893 LEU Chi-restraints excluded: chain D residue 2898 ILE Chi-restraints excluded: chain D residue 2963 PHE Chi-restraints excluded: chain D residue 3007 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 3.9990 chunk 1309 optimal weight: 0.0970 chunk 726 optimal weight: 7.9990 chunk 447 optimal weight: 0.0000 chunk 883 optimal weight: 10.0000 chunk 699 optimal weight: 9.9990 chunk 1354 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 823 optimal weight: 9.9990 chunk 1008 optimal weight: 10.0000 chunk 1569 optimal weight: 0.7980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 HIS A1452 GLN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 GLN ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 HIS B 261 HIS B 651 HIS B1452 GLN B1554 GLN B2316 ASN B2613 HIS ** B2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4933 HIS C 261 HIS C1554 GLN C2613 HIS ** C2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS D 261 HIS D 888 ASN D1452 GLN D1554 GLN D2613 HIS ** D2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4488 GLN D4933 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 141628 Z= 0.237 Angle : 0.636 20.098 191356 Z= 0.323 Chirality : 0.042 0.417 20988 Planarity : 0.005 0.141 24588 Dihedral : 6.194 76.664 19115 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 0.79 % Allowed : 5.12 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.06), residues: 17212 helix: 1.64 (0.06), residues: 8916 sheet: 0.28 (0.13), residues: 1676 loop : -0.39 (0.08), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D3250 HIS 0.019 0.001 HIS B3178 PHE 0.040 0.002 PHE A2943 TYR 0.050 0.002 TYR D2939 ARG 0.019 0.001 ARG A2336 *********************** 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 1092 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 974 time to evaluate : 11.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LEU cc_start: 0.9240 (mt) cc_final: 0.8960 (pp) REVERT: A 995 MET cc_start: 0.7968 (mtm) cc_final: 0.7602 (ttt) REVERT: A 1050 LEU cc_start: 0.9417 (mm) cc_final: 0.9098 (tp) REVERT: A 2688 MET cc_start: 0.5709 (mmt) cc_final: 0.5013 (mmt) REVERT: A 2723 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8582 (mptt) REVERT: A 2724 TYR cc_start: 0.8938 (t80) cc_final: 0.8582 (t80) REVERT: A 2757 MET cc_start: 0.7501 (mtt) cc_final: 0.6928 (mpt) REVERT: A 2772 ARG cc_start: 0.8675 (mtm110) cc_final: 0.7927 (pmm-80) REVERT: A 2782 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7582 (ppp) REVERT: A 2840 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6679 (mmt) REVERT: A 2843 MET cc_start: 0.8122 (tpt) cc_final: 0.7250 (tpt) REVERT: A 2844 MET cc_start: 0.8824 (ppp) cc_final: 0.8552 (ppp) REVERT: A 2877 LEU cc_start: 0.8812 (mt) cc_final: 0.8425 (mt) REVERT: A 2880 LYS cc_start: 0.9260 (mppt) cc_final: 0.8925 (mppt) REVERT: A 2893 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8746 (mt) REVERT: A 2895 PHE cc_start: 0.9218 (t80) cc_final: 0.8692 (t80) REVERT: A 2899 ASN cc_start: 0.8568 (m-40) cc_final: 0.7775 (m110) REVERT: A 2980 LEU cc_start: 0.8927 (tt) cc_final: 0.8655 (tm) REVERT: A 3111 HIS cc_start: 0.8194 (p-80) cc_final: 0.7410 (p-80) REVERT: A 3116 GLN cc_start: 0.9067 (tp40) cc_final: 0.8788 (tp-100) REVERT: A 3131 TYR cc_start: 0.9225 (m-10) cc_final: 0.8890 (m-80) REVERT: A 3162 PHE cc_start: 0.9137 (t80) cc_final: 0.8902 (t80) REVERT: A 3241 MET cc_start: 0.8936 (mmp) cc_final: 0.8546 (mmm) REVERT: A 3249 TRP cc_start: 0.7119 (m-90) cc_final: 0.6839 (m-90) REVERT: A 3252 HIS cc_start: 0.8308 (m90) cc_final: 0.7928 (m-70) REVERT: A 3295 TRP cc_start: 0.8119 (p-90) cc_final: 0.7542 (p-90) REVERT: A 3296 MET cc_start: 0.9190 (ptp) cc_final: 0.8559 (ptp) REVERT: E 19 LYS cc_start: 0.8760 (tppt) cc_final: 0.8525 (mmmm) REVERT: F 19 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8681 (mmmm) REVERT: H 19 LYS cc_start: 0.8877 (tppt) cc_final: 0.8598 (mmmm) REVERT: B 309 MET cc_start: 0.7907 (mmm) cc_final: 0.7637 (mpp) REVERT: B 317 MET cc_start: 0.7223 (ptt) cc_final: 0.6983 (ptt) REVERT: B 678 MET cc_start: 0.8198 (tpp) cc_final: 0.7996 (ttt) REVERT: B 940 LEU cc_start: 0.9267 (mt) cc_final: 0.8890 (pp) REVERT: B 995 MET cc_start: 0.8302 (mtm) cc_final: 0.7933 (ttt) REVERT: B 1050 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9105 (tp) REVERT: B 2719 TYR cc_start: 0.8354 (t80) cc_final: 0.7840 (t80) REVERT: B 2724 TYR cc_start: 0.8760 (t80) cc_final: 0.8249 (t80) REVERT: B 2757 MET cc_start: 0.7504 (mtt) cc_final: 0.7140 (mpt) REVERT: B 2798 MET cc_start: 0.7762 (mmm) cc_final: 0.7558 (mmm) REVERT: B 2843 MET cc_start: 0.8093 (tpt) cc_final: 0.7164 (tpt) REVERT: B 2844 MET cc_start: 0.8826 (ppp) cc_final: 0.8513 (ppp) REVERT: B 2895 PHE cc_start: 0.9132 (t80) cc_final: 0.8675 (t80) REVERT: B 2899 ASN cc_start: 0.8388 (m-40) cc_final: 0.7882 (m-40) REVERT: B 3003 MET cc_start: 0.8473 (mtp) cc_final: 0.8191 (ptp) REVERT: B 3072 MET cc_start: 0.8887 (mmm) cc_final: 0.8664 (tpp) REVERT: B 3252 HIS cc_start: 0.8261 (m90) cc_final: 0.7957 (m-70) REVERT: B 3296 MET cc_start: 0.9258 (ptp) cc_final: 0.8873 (ptp) REVERT: B 4046 ARG cc_start: 0.8891 (mpp-170) cc_final: 0.8601 (mpp-170) REVERT: B 4048 PHE cc_start: 0.8689 (t80) cc_final: 0.8325 (t80) REVERT: B 4306 PHE cc_start: 0.7585 (m-80) cc_final: 0.7238 (m-10) REVERT: C 81 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7747 (tmm) REVERT: C 317 MET cc_start: 0.7193 (ptt) cc_final: 0.6933 (ptt) REVERT: C 678 MET cc_start: 0.8133 (tpp) cc_final: 0.7783 (ttp) REVERT: C 940 LEU cc_start: 0.9160 (mt) cc_final: 0.8853 (pp) REVERT: C 995 MET cc_start: 0.7934 (mtm) cc_final: 0.7621 (ttt) REVERT: C 1050 LEU cc_start: 0.9394 (mm) cc_final: 0.9192 (mt) REVERT: C 1721 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7373 (mmp) REVERT: C 1975 MET cc_start: 0.8263 (ppp) cc_final: 0.7939 (ppp) REVERT: C 2150 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7580 (mtp) REVERT: C 2689 MET cc_start: 0.5818 (tmm) cc_final: 0.5280 (mpt) REVERT: C 2723 LYS cc_start: 0.9373 (mtpt) cc_final: 0.8910 (mmtt) REVERT: C 2724 TYR cc_start: 0.8758 (t80) cc_final: 0.8381 (t80) REVERT: C 2757 MET cc_start: 0.7563 (mtt) cc_final: 0.7030 (mpt) REVERT: C 2840 MET cc_start: 0.7020 (tpt) cc_final: 0.6324 (mmt) REVERT: C 2843 MET cc_start: 0.7763 (tpt) cc_final: 0.6856 (tpt) REVERT: C 2844 MET cc_start: 0.8711 (ppp) cc_final: 0.8467 (ppp) REVERT: C 2877 LEU cc_start: 0.8835 (mt) cc_final: 0.8430 (mt) REVERT: C 2975 PHE cc_start: 0.8670 (m-80) cc_final: 0.8413 (m-10) REVERT: C 3072 MET cc_start: 0.8552 (mmm) cc_final: 0.8350 (mmm) REVERT: C 3101 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7461 (mp) REVERT: C 3104 MET cc_start: 0.8621 (ptt) cc_final: 0.7638 (pp-130) REVERT: C 3108 LEU cc_start: 0.9302 (mt) cc_final: 0.9086 (mp) REVERT: C 3111 HIS cc_start: 0.8204 (p-80) cc_final: 0.7737 (p-80) REVERT: C 3246 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7602 (pmm) REVERT: C 3252 HIS cc_start: 0.8340 (m90) cc_final: 0.7879 (m90) REVERT: D 395 HIS cc_start: 0.7935 (m-70) cc_final: 0.7665 (m90) REVERT: D 940 LEU cc_start: 0.9470 (mt) cc_final: 0.9214 (pp) REVERT: D 995 MET cc_start: 0.8494 (mtm) cc_final: 0.8232 (mtt) REVERT: D 999 LEU cc_start: 0.9370 (mm) cc_final: 0.9028 (mt) REVERT: D 1050 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9194 (tp) REVERT: D 1168 MET cc_start: 0.8809 (mmm) cc_final: 0.8505 (mmm) REVERT: D 2192 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8031 (tpt) REVERT: D 2347 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.7497 (mpt) REVERT: D 2585 MET cc_start: 0.8559 (ttp) cc_final: 0.8294 (ttp) REVERT: D 2695 MET cc_start: 0.5896 (mmm) cc_final: 0.5289 (mmm) REVERT: D 2724 TYR cc_start: 0.9031 (t80) cc_final: 0.8512 (t80) REVERT: D 2727 HIS cc_start: 0.9272 (t-170) cc_final: 0.9057 (t-90) REVERT: D 2757 MET cc_start: 0.7423 (mtt) cc_final: 0.7002 (mpp) REVERT: D 2772 ARG cc_start: 0.9211 (mtm180) cc_final: 0.8901 (mtm110) REVERT: D 2782 MET cc_start: 0.7959 (ptm) cc_final: 0.7648 (ptt) REVERT: D 2785 TRP cc_start: 0.7701 (m-10) cc_final: 0.6866 (m-10) REVERT: D 2798 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7462 (mpm) REVERT: D 2843 MET cc_start: 0.8609 (tpt) cc_final: 0.7659 (tpt) REVERT: D 2844 MET cc_start: 0.8720 (ppp) cc_final: 0.8480 (ppp) REVERT: D 2847 ASN cc_start: 0.9318 (t0) cc_final: 0.8944 (t0) REVERT: D 2856 LYS cc_start: 0.8005 (mptt) cc_final: 0.7544 (mptt) REVERT: D 2880 LYS cc_start: 0.9177 (mppt) cc_final: 0.8825 (mppt) REVERT: D 2898 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8836 (pt) REVERT: D 2901 TYR cc_start: 0.7650 (m-10) cc_final: 0.7295 (m-10) REVERT: D 2939 TYR cc_start: 0.8594 (m-80) cc_final: 0.8369 (m-80) REVERT: D 2980 LEU cc_start: 0.8859 (tt) cc_final: 0.8552 (tm) REVERT: D 3003 MET cc_start: 0.8494 (mtm) cc_final: 0.8150 (mtp) REVERT: D 3007 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8750 (mt) REVERT: D 3057 LEU cc_start: 0.9104 (tm) cc_final: 0.8799 (pp) REVERT: D 3101 LEU cc_start: 0.8314 (mp) cc_final: 0.7995 (mm) REVERT: D 3131 TYR cc_start: 0.8842 (m-10) cc_final: 0.8587 (m-80) REVERT: D 3162 PHE cc_start: 0.9025 (t80) cc_final: 0.8706 (t80) REVERT: D 3231 MET cc_start: 0.9214 (tpt) cc_final: 0.8942 (tpp) REVERT: D 3252 HIS cc_start: 0.8011 (m90) cc_final: 0.7682 (m-70) REVERT: D 3273 MET cc_start: 0.9262 (mmm) cc_final: 0.9026 (mmm) REVERT: D 3295 TRP cc_start: 0.7685 (p-90) cc_final: 0.7120 (p-90) REVERT: D 3296 MET cc_start: 0.9113 (ptp) cc_final: 0.8418 (ptp) REVERT: D 3819 MET cc_start: 0.6118 (pmt) cc_final: 0.5868 (pmt) REVERT: D 4048 PHE cc_start: 0.8448 (t80) cc_final: 0.8144 (t80) REVERT: D 4305 PHE cc_start: 0.7992 (t80) cc_final: 0.7740 (t80) REVERT: D 4306 PHE cc_start: 0.7504 (m-80) cc_final: 0.7118 (m-10) outliers start: 118 outliers final: 19 residues processed: 994 average time/residue: 1.9709 time to fit residues: 2854.0355 Evaluate side-chains 956 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 922 time to evaluate : 11.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2782 MET Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2963 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2594 PHE Chi-restraints excluded: chain C residue 2963 PHE Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 1060 TYR Chi-restraints excluded: chain D residue 2175 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2798 MET Chi-restraints excluded: chain D residue 2898 ILE Chi-restraints excluded: chain D residue 3007 LEU Chi-restraints excluded: chain D residue 3246 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 7.9990 chunk 487 optimal weight: 0.3980 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 3.9990 chunk 432 optimal weight: 4.9990 chunk 1572 optimal weight: 5.9990 chunk 1698 optimal weight: 1.9990 chunk 1400 optimal weight: 20.0000 chunk 1558 optimal weight: 30.0000 chunk 535 optimal weight: 1.9990 chunk 1261 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3269 ASN C1452 GLN ** C2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3269 ASN C4488 GLN D 651 HIS D 930 ASN ** D2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 141628 Z= 0.232 Angle : 0.605 14.973 191356 Z= 0.306 Chirality : 0.041 0.426 20988 Planarity : 0.005 0.132 24588 Dihedral : 5.754 75.539 19044 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 0.80 % Allowed : 6.12 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.06), residues: 17212 helix: 1.78 (0.06), residues: 8920 sheet: 0.22 (0.13), residues: 1640 loop : -0.39 (0.08), residues: 6652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D2852 HIS 0.019 0.001 HIS C3178 PHE 0.046 0.002 PHE B2943 TYR 0.043 0.001 TYR C 931 ARG 0.015 0.000 ARG E 14 *********************** 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 1074 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 957 time to evaluate : 11.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LEU cc_start: 0.9337 (mt) cc_final: 0.9025 (pp) REVERT: A 995 MET cc_start: 0.8007 (mtm) cc_final: 0.7584 (ttt) REVERT: A 1050 LEU cc_start: 0.9388 (mm) cc_final: 0.9059 (tp) REVERT: A 2150 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: A 2234 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (mtt) REVERT: A 2456 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7876 (tpp) REVERT: A 2724 TYR cc_start: 0.8988 (t80) cc_final: 0.8582 (t80) REVERT: A 2757 MET cc_start: 0.7285 (mtt) cc_final: 0.6820 (mpt) REVERT: A 2772 ARG cc_start: 0.8637 (mtm110) cc_final: 0.7997 (pmm-80) REVERT: A 2782 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7658 (ppp) REVERT: A 2798 MET cc_start: 0.7648 (mmm) cc_final: 0.7345 (mpm) REVERT: A 2840 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6685 (mmt) REVERT: A 2843 MET cc_start: 0.8152 (tpt) cc_final: 0.7572 (tpt) REVERT: A 2844 MET cc_start: 0.8878 (ppp) cc_final: 0.8573 (ppp) REVERT: A 2877 LEU cc_start: 0.8814 (mt) cc_final: 0.8421 (mt) REVERT: A 2880 LYS cc_start: 0.9270 (mppt) cc_final: 0.8922 (mppt) REVERT: A 2893 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8746 (mp) REVERT: A 2895 PHE cc_start: 0.9200 (t80) cc_final: 0.8790 (t80) REVERT: A 2939 TYR cc_start: 0.8629 (m-80) cc_final: 0.8425 (m-80) REVERT: A 2980 LEU cc_start: 0.8982 (tt) cc_final: 0.8712 (tm) REVERT: A 3034 HIS cc_start: 0.8411 (m90) cc_final: 0.8054 (m90) REVERT: A 3057 LEU cc_start: 0.9332 (tm) cc_final: 0.8963 (pp) REVERT: A 3111 HIS cc_start: 0.8192 (p-80) cc_final: 0.7467 (p90) REVERT: A 3116 GLN cc_start: 0.9028 (tp40) cc_final: 0.8802 (tp-100) REVERT: A 3131 TYR cc_start: 0.9203 (m-10) cc_final: 0.8913 (m-80) REVERT: A 3162 PHE cc_start: 0.9113 (t80) cc_final: 0.8673 (t80) REVERT: A 3241 MET cc_start: 0.9048 (mmp) cc_final: 0.8625 (mmm) REVERT: A 3246 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7788 (mtm) REVERT: A 3252 HIS cc_start: 0.8319 (m90) cc_final: 0.7953 (m-70) REVERT: A 3295 TRP cc_start: 0.8183 (p-90) cc_final: 0.7808 (p-90) REVERT: A 3296 MET cc_start: 0.9203 (ptp) cc_final: 0.8519 (ptp) REVERT: A 4052 MET cc_start: 0.8345 (mtp) cc_final: 0.8113 (mtm) REVERT: G 50 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7714 (mtp180) REVERT: H 19 LYS cc_start: 0.8896 (tppt) cc_final: 0.8679 (mmmm) REVERT: B 940 LEU cc_start: 0.9292 (mt) cc_final: 0.8978 (pp) REVERT: B 995 MET cc_start: 0.8320 (mtm) cc_final: 0.7880 (ttt) REVERT: B 1050 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9174 (tp) REVERT: B 2150 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7760 (mpp) REVERT: B 2192 MET cc_start: 0.8537 (tpp) cc_final: 0.8260 (tpt) REVERT: B 2719 TYR cc_start: 0.8407 (t80) cc_final: 0.7832 (t80) REVERT: B 2724 TYR cc_start: 0.8675 (t80) cc_final: 0.8332 (t80) REVERT: B 2757 MET cc_start: 0.7359 (mtt) cc_final: 0.7041 (mpt) REVERT: B 2798 MET cc_start: 0.7736 (mmm) cc_final: 0.7297 (mmm) REVERT: B 2840 MET cc_start: 0.7073 (mmt) cc_final: 0.6645 (mmt) REVERT: B 2843 MET cc_start: 0.8075 (tpt) cc_final: 0.7527 (tpt) REVERT: B 2844 MET cc_start: 0.8849 (ppp) cc_final: 0.8518 (ppp) REVERT: B 3072 MET cc_start: 0.8877 (mmm) cc_final: 0.8608 (tpp) REVERT: B 3117 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8246 (t80) REVERT: B 3214 LEU cc_start: 0.9517 (mm) cc_final: 0.9272 (mp) REVERT: B 3252 HIS cc_start: 0.8228 (m90) cc_final: 0.7823 (m-70) REVERT: B 3295 TRP cc_start: 0.8491 (p-90) cc_final: 0.8063 (p-90) REVERT: B 3296 MET cc_start: 0.9256 (ptp) cc_final: 0.8855 (ptp) REVERT: B 4048 PHE cc_start: 0.8668 (t80) cc_final: 0.8391 (t80) REVERT: B 4258 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7999 (ptm) REVERT: B 4306 PHE cc_start: 0.7611 (m-80) cc_final: 0.7234 (m-10) REVERT: C 81 MET cc_start: 0.7954 (ppp) cc_final: 0.7739 (tmm) REVERT: C 317 MET cc_start: 0.7236 (ptt) cc_final: 0.7003 (ptt) REVERT: C 678 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7854 (ttp) REVERT: C 940 LEU cc_start: 0.9234 (mt) cc_final: 0.8925 (pp) REVERT: C 964 MET cc_start: 0.1312 (OUTLIER) cc_final: 0.0828 (pmm) REVERT: C 995 MET cc_start: 0.7863 (mtm) cc_final: 0.7535 (ttt) REVERT: C 1050 LEU cc_start: 0.9421 (mm) cc_final: 0.9210 (mt) REVERT: C 2723 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8947 (mmtt) REVERT: C 2724 TYR cc_start: 0.8756 (t80) cc_final: 0.8329 (t80) REVERT: C 2757 MET cc_start: 0.7364 (mtt) cc_final: 0.6924 (mpt) REVERT: C 2782 MET cc_start: 0.8324 (ptm) cc_final: 0.8057 (ppp) REVERT: C 2840 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6130 (mmt) REVERT: C 2843 MET cc_start: 0.7825 (tpt) cc_final: 0.7114 (tpt) REVERT: C 2844 MET cc_start: 0.8790 (ppp) cc_final: 0.8499 (ppp) REVERT: C 2877 LEU cc_start: 0.8839 (mt) cc_final: 0.8438 (mt) REVERT: C 2975 PHE cc_start: 0.8666 (m-10) cc_final: 0.8378 (m-10) REVERT: C 3072 MET cc_start: 0.8653 (mmm) cc_final: 0.8452 (mmm) REVERT: C 3101 LEU cc_start: 0.8068 (mt) cc_final: 0.7721 (mm) REVERT: C 3104 MET cc_start: 0.8625 (ptt) cc_final: 0.7632 (pp-130) REVERT: C 3108 LEU cc_start: 0.9304 (mt) cc_final: 0.9056 (mp) REVERT: C 3111 HIS cc_start: 0.8263 (p-80) cc_final: 0.7783 (p-80) REVERT: C 3117 PHE cc_start: 0.8889 (m-80) cc_final: 0.8678 (t80) REVERT: C 3246 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7879 (pmm) REVERT: C 3249 TRP cc_start: 0.7726 (m-10) cc_final: 0.7502 (m-10) REVERT: C 3250 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (m100) REVERT: C 3252 HIS cc_start: 0.8283 (m90) cc_final: 0.7874 (m90) REVERT: D 395 HIS cc_start: 0.7951 (m-70) cc_final: 0.7611 (m170) REVERT: D 940 LEU cc_start: 0.9465 (mt) cc_final: 0.9158 (pp) REVERT: D 995 MET cc_start: 0.8553 (mtm) cc_final: 0.8260 (mtt) REVERT: D 999 LEU cc_start: 0.9312 (mm) cc_final: 0.9052 (mt) REVERT: D 1050 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9236 (tp) REVERT: D 1168 MET cc_start: 0.8784 (mmm) cc_final: 0.8266 (mmm) REVERT: D 2150 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7205 (mtp) REVERT: D 2192 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8018 (tpt) REVERT: D 2347 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.7517 (mpt) REVERT: D 2662 PHE cc_start: 0.7986 (m-10) cc_final: 0.7786 (m-10) REVERT: D 2681 MET cc_start: 0.6557 (mpm) cc_final: 0.6236 (tmt) REVERT: D 2724 TYR cc_start: 0.9013 (t80) cc_final: 0.8627 (t80) REVERT: D 2727 HIS cc_start: 0.9236 (t-170) cc_final: 0.8781 (m170) REVERT: D 2757 MET cc_start: 0.7025 (mtt) cc_final: 0.6643 (mpp) REVERT: D 2782 MET cc_start: 0.8044 (ptm) cc_final: 0.7573 (ptm) REVERT: D 2840 MET cc_start: 0.7743 (mmt) cc_final: 0.7343 (mmt) REVERT: D 2843 MET cc_start: 0.8665 (tpt) cc_final: 0.7805 (tpt) REVERT: D 2856 LYS cc_start: 0.8142 (mptt) cc_final: 0.7731 (mptp) REVERT: D 2880 LYS cc_start: 0.9195 (mppt) cc_final: 0.8815 (mppt) REVERT: D 2898 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8809 (pt) REVERT: D 2899 ASN cc_start: 0.7903 (p0) cc_final: 0.6629 (p0) REVERT: D 2901 TYR cc_start: 0.7372 (m-10) cc_final: 0.6832 (m-10) REVERT: D 2939 TYR cc_start: 0.8566 (m-80) cc_final: 0.8289 (m-80) REVERT: D 2980 LEU cc_start: 0.8883 (tt) cc_final: 0.8554 (tm) REVERT: D 3007 LEU cc_start: 0.9005 (mt) cc_final: 0.8742 (mt) REVERT: D 3057 LEU cc_start: 0.9125 (tm) cc_final: 0.8778 (pp) REVERT: D 3131 TYR cc_start: 0.8843 (m-10) cc_final: 0.8588 (m-80) REVERT: D 3162 PHE cc_start: 0.9068 (t80) cc_final: 0.8773 (t80) REVERT: D 3231 MET cc_start: 0.9154 (tpt) cc_final: 0.8944 (tpp) REVERT: D 3252 HIS cc_start: 0.7989 (m90) cc_final: 0.7570 (m-70) REVERT: D 3296 MET cc_start: 0.9134 (ptp) cc_final: 0.8687 (ptt) REVERT: D 3819 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5736 (pmt) REVERT: D 4048 PHE cc_start: 0.8444 (t80) cc_final: 0.8191 (t80) REVERT: D 4305 PHE cc_start: 0.8054 (t80) cc_final: 0.7785 (t80) REVERT: D 4306 PHE cc_start: 0.7471 (m-80) cc_final: 0.7115 (m-10) outliers start: 117 outliers final: 39 residues processed: 986 average time/residue: 2.0180 time to fit residues: 2898.1959 Evaluate side-chains 985 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 924 time to evaluate : 11.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2456 MET Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2782 MET Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 3021 LEU Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3117 PHE Chi-restraints excluded: chain B residue 3181 TYR Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4264 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2932 TYR Chi-restraints excluded: chain C residue 2963 PHE Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3250 TRP Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 1050 LEU Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2898 ILE Chi-restraints excluded: chain D residue 3146 ILE Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3819 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 4.9990 chunk 1181 optimal weight: 0.7980 chunk 815 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 750 optimal weight: 50.0000 chunk 1055 optimal weight: 6.9990 chunk 1577 optimal weight: 3.9990 chunk 1670 optimal weight: 3.9990 chunk 824 optimal weight: 8.9990 chunk 1495 optimal weight: 4.9990 chunk 450 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1939 ASN ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2754 GLN ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3269 ASN A4488 GLN H 26 HIS B 930 ASN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 ASN ** B2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2754 GLN ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4488 GLN C2754 GLN C3017 HIS ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 HIS C3269 ASN ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1939 ASN D2754 GLN ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3233 HIS ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 141628 Z= 0.291 Angle : 0.615 15.713 191356 Z= 0.310 Chirality : 0.041 0.391 20988 Planarity : 0.005 0.130 24588 Dihedral : 5.614 76.765 19038 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 1.11 % Allowed : 6.86 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.06), residues: 17212 helix: 1.79 (0.05), residues: 8952 sheet: 0.22 (0.13), residues: 1592 loop : -0.37 (0.08), residues: 6668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D2852 HIS 0.014 0.001 HIS C3178 PHE 0.047 0.002 PHE A3117 TYR 0.044 0.002 TYR A 931 ARG 0.013 0.001 ARG C2772 *********************** 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 1122 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 959 time to evaluate : 11.566 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: A 940 LEU cc_start: 0.9305 (mt) cc_final: 0.9002 (pp) REVERT: A 946 LEU cc_start: 0.8334 (mt) cc_final: 0.7829 (pp) REVERT: A 995 MET cc_start: 0.8003 (mtm) cc_final: 0.7565 (mtt) REVERT: A 1050 LEU cc_start: 0.9387 (mm) cc_final: 0.9048 (tp) REVERT: A 1975 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7972 (ppp) REVERT: A 2142 MET cc_start: 0.8161 (tpt) cc_final: 0.7896 (tpp) REVERT: A 2150 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7220 (mpp) REVERT: A 2689 MET cc_start: 0.6067 (tmm) cc_final: 0.5377 (mpp) REVERT: A 2723 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8449 (tmtt) REVERT: A 2724 TYR cc_start: 0.8987 (t80) cc_final: 0.8603 (t80) REVERT: A 2757 MET cc_start: 0.7278 (mtt) cc_final: 0.6781 (mpt) REVERT: A 2840 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6696 (mmt) REVERT: A 2843 MET cc_start: 0.8229 (tpt) cc_final: 0.7303 (tpt) REVERT: A 2844 MET cc_start: 0.8929 (ppp) cc_final: 0.8621 (ppp) REVERT: A 2877 LEU cc_start: 0.8822 (mt) cc_final: 0.8426 (mt) REVERT: A 2880 LYS cc_start: 0.9277 (mppt) cc_final: 0.8958 (mppt) REVERT: A 2895 PHE cc_start: 0.9194 (t80) cc_final: 0.8569 (t80) REVERT: A 2939 TYR cc_start: 0.8519 (m-80) cc_final: 0.8284 (m-80) REVERT: A 2980 LEU cc_start: 0.9031 (tt) cc_final: 0.8760 (tm) REVERT: A 3003 MET cc_start: 0.8663 (ptm) cc_final: 0.8413 (ptm) REVERT: A 3034 HIS cc_start: 0.8412 (m90) cc_final: 0.8042 (m90) REVERT: A 3131 TYR cc_start: 0.9241 (m-10) cc_final: 0.8864 (m-80) REVERT: A 3241 MET cc_start: 0.9045 (mmp) cc_final: 0.8630 (mmm) REVERT: A 3246 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7786 (pmm) REVERT: A 3252 HIS cc_start: 0.8301 (m90) cc_final: 0.8010 (m90) REVERT: A 3296 MET cc_start: 0.9208 (ptp) cc_final: 0.8824 (ptt) REVERT: A 3819 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5757 (pmt) REVERT: G 50 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7746 (mtp180) REVERT: B 309 MET cc_start: 0.7546 (mmp) cc_final: 0.7285 (mpp) REVERT: B 940 LEU cc_start: 0.9307 (mt) cc_final: 0.8994 (pp) REVERT: B 995 MET cc_start: 0.8349 (mtm) cc_final: 0.7919 (ttt) REVERT: B 1050 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9222 (tp) REVERT: B 1729 MET cc_start: 0.7931 (tpp) cc_final: 0.7698 (mmt) REVERT: B 2150 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7684 (mpp) REVERT: B 2689 MET cc_start: 0.5471 (tmm) cc_final: 0.5018 (mpt) REVERT: B 2723 LYS cc_start: 0.9325 (mtpt) cc_final: 0.8472 (mmtt) REVERT: B 2724 TYR cc_start: 0.8873 (t80) cc_final: 0.8554 (t80) REVERT: B 2730 ASP cc_start: 0.9212 (m-30) cc_final: 0.8883 (t0) REVERT: B 2757 MET cc_start: 0.7313 (mtt) cc_final: 0.6974 (mpt) REVERT: B 2772 ARG cc_start: 0.8324 (mmm160) cc_final: 0.7994 (tpp80) REVERT: B 2798 MET cc_start: 0.8030 (mmm) cc_final: 0.7724 (mmm) REVERT: B 2843 MET cc_start: 0.8189 (tpt) cc_final: 0.7281 (tpt) REVERT: B 2844 MET cc_start: 0.8919 (ppp) cc_final: 0.8608 (ppp) REVERT: B 2895 PHE cc_start: 0.9104 (t80) cc_final: 0.7727 (t80) REVERT: B 2939 TYR cc_start: 0.8645 (m-80) cc_final: 0.8437 (m-80) REVERT: B 3072 MET cc_start: 0.8836 (mmm) cc_final: 0.8593 (tpp) REVERT: B 3108 LEU cc_start: 0.9149 (mt) cc_final: 0.8885 (mm) REVERT: B 3250 TRP cc_start: 0.7791 (m100) cc_final: 0.7563 (m100) REVERT: B 3252 HIS cc_start: 0.8252 (m90) cc_final: 0.7845 (m-70) REVERT: B 3295 TRP cc_start: 0.8563 (p-90) cc_final: 0.8174 (p-90) REVERT: B 3296 MET cc_start: 0.9247 (ptp) cc_final: 0.8797 (ptp) REVERT: B 3819 MET cc_start: 0.5876 (pmt) cc_final: 0.5580 (pmt) REVERT: B 4048 PHE cc_start: 0.8740 (t80) cc_final: 0.8485 (t80) REVERT: B 4258 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7940 (ptm) REVERT: B 4306 PHE cc_start: 0.7577 (m-80) cc_final: 0.7170 (m-10) REVERT: C 678 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7909 (ttp) REVERT: C 940 LEU cc_start: 0.9242 (mt) cc_final: 0.8966 (pp) REVERT: C 995 MET cc_start: 0.7899 (mtm) cc_final: 0.7382 (ttt) REVERT: C 999 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8818 (mm) REVERT: C 1050 LEU cc_start: 0.9420 (mm) cc_final: 0.9157 (tp) REVERT: C 1168 MET cc_start: 0.8354 (mmm) cc_final: 0.8133 (mmp) REVERT: C 1721 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7536 (mmp) REVERT: C 2150 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7396 (mpp) REVERT: C 2681 MET cc_start: 0.7542 (mmm) cc_final: 0.7231 (tmm) REVERT: C 2688 MET cc_start: 0.6255 (mmt) cc_final: 0.5621 (mpp) REVERT: C 2689 MET cc_start: 0.5851 (tmm) cc_final: 0.5142 (mpt) REVERT: C 2723 LYS cc_start: 0.9349 (mtpt) cc_final: 0.8948 (mmtt) REVERT: C 2727 HIS cc_start: 0.9413 (t-170) cc_final: 0.9121 (t-170) REVERT: C 2757 MET cc_start: 0.7268 (mtt) cc_final: 0.6869 (mpt) REVERT: C 2782 MET cc_start: 0.8353 (ptm) cc_final: 0.8120 (ppp) REVERT: C 2840 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6222 (mmt) REVERT: C 2843 MET cc_start: 0.7885 (tpt) cc_final: 0.7045 (tpt) REVERT: C 2844 MET cc_start: 0.8853 (ppp) cc_final: 0.8538 (ppp) REVERT: C 2877 LEU cc_start: 0.8856 (mt) cc_final: 0.8466 (mt) REVERT: C 2880 LYS cc_start: 0.9295 (mppt) cc_final: 0.9043 (mppt) REVERT: C 2975 PHE cc_start: 0.8675 (m-10) cc_final: 0.8376 (m-10) REVERT: C 3072 MET cc_start: 0.8655 (mmm) cc_final: 0.8443 (mmm) REVERT: C 3101 LEU cc_start: 0.8084 (mt) cc_final: 0.7823 (mm) REVERT: C 3104 MET cc_start: 0.8637 (ptt) cc_final: 0.7660 (pp-130) REVERT: C 3108 LEU cc_start: 0.9306 (mt) cc_final: 0.9061 (mp) REVERT: C 3111 HIS cc_start: 0.8263 (p-80) cc_final: 0.7913 (p90) REVERT: C 3131 TYR cc_start: 0.9197 (m-10) cc_final: 0.8940 (m-10) REVERT: C 3246 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7793 (pmm) REVERT: C 3252 HIS cc_start: 0.8339 (m90) cc_final: 0.7993 (m-70) REVERT: C 3269 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8597 (p0) REVERT: C 3272 HIS cc_start: 0.8503 (m90) cc_final: 0.8057 (m90) REVERT: D 395 HIS cc_start: 0.7971 (m-70) cc_final: 0.7621 (m-70) REVERT: D 995 MET cc_start: 0.8592 (mtm) cc_final: 0.8250 (mtt) REVERT: D 1168 MET cc_start: 0.8716 (mmm) cc_final: 0.8195 (mmt) REVERT: D 2192 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8075 (tpt) REVERT: D 2347 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.7528 (mpt) REVERT: D 2585 MET cc_start: 0.8694 (ttp) cc_final: 0.8460 (ttp) REVERT: D 2724 TYR cc_start: 0.9019 (t80) cc_final: 0.8607 (t80) REVERT: D 2727 HIS cc_start: 0.9241 (t-170) cc_final: 0.8842 (m170) REVERT: D 2757 MET cc_start: 0.6974 (mtt) cc_final: 0.6662 (mpp) REVERT: D 2782 MET cc_start: 0.8085 (ptm) cc_final: 0.7585 (ptm) REVERT: D 2798 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7268 (mpm) REVERT: D 2843 MET cc_start: 0.8670 (tpt) cc_final: 0.7743 (tpt) REVERT: D 2847 ASN cc_start: 0.9380 (t0) cc_final: 0.9159 (t0) REVERT: D 2856 LYS cc_start: 0.8385 (mptt) cc_final: 0.7991 (mptp) REVERT: D 2880 LYS cc_start: 0.9224 (mppt) cc_final: 0.8832 (mppt) REVERT: D 2898 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8897 (tp) REVERT: D 2980 LEU cc_start: 0.8948 (tt) cc_final: 0.8629 (tm) REVERT: D 3007 LEU cc_start: 0.9015 (mt) cc_final: 0.8758 (mt) REVERT: D 3057 LEU cc_start: 0.9131 (tm) cc_final: 0.8807 (pp) REVERT: D 3131 TYR cc_start: 0.8834 (m-10) cc_final: 0.8586 (m-80) REVERT: D 3137 LEU cc_start: 0.9467 (mm) cc_final: 0.9207 (mp) REVERT: D 3162 PHE cc_start: 0.9048 (t80) cc_final: 0.8775 (t80) REVERT: D 3231 MET cc_start: 0.9114 (tpt) cc_final: 0.8903 (tpp) REVERT: D 3252 HIS cc_start: 0.8008 (m90) cc_final: 0.7617 (m-70) REVERT: D 3263 MET cc_start: 0.8420 (mmm) cc_final: 0.7900 (mpm) REVERT: D 3273 MET cc_start: 0.9178 (mpm) cc_final: 0.8824 (mpm) REVERT: D 3295 TRP cc_start: 0.7673 (p-90) cc_final: 0.7408 (p-90) REVERT: D 3296 MET cc_start: 0.9083 (ptp) cc_final: 0.8647 (ptp) REVERT: D 3819 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5704 (pmt) REVERT: D 4305 PHE cc_start: 0.8094 (t80) cc_final: 0.7808 (t80) REVERT: D 4306 PHE cc_start: 0.7458 (m-80) cc_final: 0.7109 (m-10) outliers start: 163 outliers final: 44 residues processed: 1022 average time/residue: 1.9946 time to fit residues: 2975.6139 Evaluate side-chains 993 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 929 time to evaluate : 11.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2771 TYR Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 2963 PHE Chi-restraints excluded: chain A residue 3021 LEU Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3819 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4264 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2775 ILE Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3269 ASN Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 1035 TYR Chi-restraints excluded: chain D residue 1060 TYR Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2652 LEU Chi-restraints excluded: chain D residue 2798 MET Chi-restraints excluded: chain D residue 2898 ILE Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3250 TRP Chi-restraints excluded: chain D residue 3653 GLU Chi-restraints excluded: chain D residue 3819 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 3.9990 chunk 948 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 1243 optimal weight: 0.4980 chunk 689 optimal weight: 10.0000 chunk 1425 optimal weight: 5.9990 chunk 1154 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 chunk 852 optimal weight: 1.9990 chunk 1499 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3233 HIS A3269 ASN E 26 HIS H 26 HIS ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 ASN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3269 ASN ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2316 ASN D2727 HIS ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 141628 Z= 0.273 Angle : 0.615 18.426 191356 Z= 0.308 Chirality : 0.041 0.412 20988 Planarity : 0.005 0.128 24588 Dihedral : 5.521 76.802 19034 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 0.95 % Allowed : 7.75 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.06), residues: 17212 helix: 1.82 (0.05), residues: 8952 sheet: 0.22 (0.13), residues: 1644 loop : -0.37 (0.08), residues: 6616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A3295 HIS 0.017 0.001 HIS B2727 PHE 0.056 0.002 PHE A3117 TYR 0.047 0.001 TYR C 931 ARG 0.011 0.000 ARG E 14 *********************** 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 1092 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 953 time to evaluate : 11.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LEU cc_start: 0.9305 (mt) cc_final: 0.8987 (pp) REVERT: A 946 LEU cc_start: 0.8420 (mt) cc_final: 0.7948 (pp) REVERT: A 995 MET cc_start: 0.8036 (mtm) cc_final: 0.7628 (mtt) REVERT: A 1050 LEU cc_start: 0.9370 (mm) cc_final: 0.9038 (tp) REVERT: A 1168 MET cc_start: 0.8333 (mmm) cc_final: 0.8110 (mmp) REVERT: A 1975 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7987 (ppp) REVERT: A 2142 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: A 2150 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: A 2584 MET cc_start: 0.8258 (ptm) cc_final: 0.8041 (ptm) REVERT: A 2689 MET cc_start: 0.6019 (tmm) cc_final: 0.5461 (mpt) REVERT: A 2724 TYR cc_start: 0.8978 (t80) cc_final: 0.8597 (t80) REVERT: A 2757 MET cc_start: 0.7208 (mtt) cc_final: 0.6742 (mpt) REVERT: A 2782 MET cc_start: 0.8372 (ptm) cc_final: 0.8061 (ppp) REVERT: A 2798 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6728 (mpm) REVERT: A 2840 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6896 (mmt) REVERT: A 2843 MET cc_start: 0.8215 (tpt) cc_final: 0.7363 (tpt) REVERT: A 2844 MET cc_start: 0.8912 (ppp) cc_final: 0.8586 (ppp) REVERT: A 2877 LEU cc_start: 0.8825 (mt) cc_final: 0.8435 (mt) REVERT: A 2880 LYS cc_start: 0.9280 (mppt) cc_final: 0.8961 (mppt) REVERT: A 2895 PHE cc_start: 0.9162 (t80) cc_final: 0.8869 (t80) REVERT: A 2939 TYR cc_start: 0.8563 (m-80) cc_final: 0.8271 (m-80) REVERT: A 2980 LEU cc_start: 0.9027 (tt) cc_final: 0.8753 (tm) REVERT: A 3003 MET cc_start: 0.8704 (ptm) cc_final: 0.8343 (ptm) REVERT: A 3021 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6619 (mp) REVERT: A 3034 HIS cc_start: 0.8414 (m90) cc_final: 0.8069 (m90) REVERT: A 3117 PHE cc_start: 0.8430 (t80) cc_final: 0.8109 (t80) REVERT: A 3131 TYR cc_start: 0.9243 (m-10) cc_final: 0.8864 (m-80) REVERT: A 3241 MET cc_start: 0.9068 (mmp) cc_final: 0.8623 (mmm) REVERT: A 3246 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7795 (pmm) REVERT: A 3252 HIS cc_start: 0.8304 (m90) cc_final: 0.7918 (m-70) REVERT: A 3295 TRP cc_start: 0.8055 (p-90) cc_final: 0.7581 (p-90) REVERT: A 3296 MET cc_start: 0.9161 (ptp) cc_final: 0.8700 (ptp) REVERT: A 4258 MET cc_start: 0.8156 (ptp) cc_final: 0.7922 (ptm) REVERT: F 26 HIS cc_start: 0.9304 (OUTLIER) cc_final: 0.8616 (m-70) REVERT: G 50 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7747 (mtp180) REVERT: B 309 MET cc_start: 0.7561 (mmp) cc_final: 0.7267 (mpp) REVERT: B 940 LEU cc_start: 0.9300 (mt) cc_final: 0.8990 (pp) REVERT: B 995 MET cc_start: 0.8375 (mtm) cc_final: 0.7947 (ttt) REVERT: B 1050 LEU cc_start: 0.9519 (mp) cc_final: 0.9226 (tp) REVERT: B 1165 MET cc_start: 0.8432 (mpp) cc_final: 0.8208 (mtm) REVERT: B 1729 MET cc_start: 0.7996 (tpp) cc_final: 0.7635 (mmt) REVERT: B 2456 MET cc_start: 0.8747 (mmm) cc_final: 0.8527 (tpp) REVERT: B 2689 MET cc_start: 0.5495 (tmm) cc_final: 0.5046 (mpm) REVERT: B 2695 MET cc_start: 0.4269 (mmm) cc_final: 0.3847 (mmm) REVERT: B 2723 LYS cc_start: 0.9213 (mtpt) cc_final: 0.8518 (mmpt) REVERT: B 2724 TYR cc_start: 0.8871 (t80) cc_final: 0.8606 (t80) REVERT: B 2727 HIS cc_start: 0.8734 (m-70) cc_final: 0.8299 (m170) REVERT: B 2730 ASP cc_start: 0.9243 (m-30) cc_final: 0.8849 (OUTLIER) REVERT: B 2734 MET cc_start: 0.9600 (mmp) cc_final: 0.9360 (mmp) REVERT: B 2757 MET cc_start: 0.7176 (mtt) cc_final: 0.6851 (mpt) REVERT: B 2772 ARG cc_start: 0.8276 (mmm160) cc_final: 0.8053 (tpp80) REVERT: B 2840 MET cc_start: 0.7267 (mmt) cc_final: 0.6903 (mmt) REVERT: B 2843 MET cc_start: 0.8186 (tpt) cc_final: 0.7355 (tpt) REVERT: B 2844 MET cc_start: 0.8940 (ppp) cc_final: 0.8644 (ppp) REVERT: B 2895 PHE cc_start: 0.8806 (t80) cc_final: 0.8240 (t80) REVERT: B 2939 TYR cc_start: 0.8583 (m-80) cc_final: 0.8339 (m-80) REVERT: B 3072 MET cc_start: 0.8794 (mmm) cc_final: 0.8542 (tpp) REVERT: B 3108 LEU cc_start: 0.9161 (mt) cc_final: 0.8886 (mm) REVERT: B 3252 HIS cc_start: 0.8276 (m90) cc_final: 0.7837 (m-70) REVERT: B 3295 TRP cc_start: 0.8583 (p-90) cc_final: 0.8146 (p-90) REVERT: B 3296 MET cc_start: 0.9237 (ptp) cc_final: 0.8708 (ptp) REVERT: B 3819 MET cc_start: 0.5856 (pmt) cc_final: 0.5563 (pmt) REVERT: B 4048 PHE cc_start: 0.8723 (t80) cc_final: 0.8500 (t80) REVERT: B 4258 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7804 (ptm) REVERT: B 4306 PHE cc_start: 0.7577 (m-80) cc_final: 0.7171 (m-10) REVERT: C 678 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7900 (ttp) REVERT: C 940 LEU cc_start: 0.9242 (mt) cc_final: 0.8931 (pp) REVERT: C 995 MET cc_start: 0.7900 (mtm) cc_final: 0.7303 (ttt) REVERT: C 999 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 1050 LEU cc_start: 0.9429 (mm) cc_final: 0.9171 (tp) REVERT: C 1721 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7527 (mmp) REVERT: C 2150 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: C 2723 LYS cc_start: 0.9340 (mtpt) cc_final: 0.8918 (mppt) REVERT: C 2757 MET cc_start: 0.7239 (mtt) cc_final: 0.6847 (mpt) REVERT: C 2772 ARG cc_start: 0.8276 (mmm160) cc_final: 0.8066 (mmm160) REVERT: C 2782 MET cc_start: 0.8450 (ptm) cc_final: 0.8144 (ppp) REVERT: C 2840 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6345 (mmt) REVERT: C 2843 MET cc_start: 0.7933 (tpt) cc_final: 0.7276 (tpt) REVERT: C 2844 MET cc_start: 0.8874 (ppp) cc_final: 0.8540 (ppp) REVERT: C 2877 LEU cc_start: 0.8851 (mt) cc_final: 0.8469 (mt) REVERT: C 2880 LYS cc_start: 0.9292 (mppt) cc_final: 0.9042 (mppt) REVERT: C 2895 PHE cc_start: 0.9143 (t80) cc_final: 0.8937 (t80) REVERT: C 2974 TYR cc_start: 0.8301 (t80) cc_final: 0.8074 (t80) REVERT: C 2975 PHE cc_start: 0.8601 (m-10) cc_final: 0.8286 (m-10) REVERT: C 3003 MET cc_start: 0.8573 (ptm) cc_final: 0.8163 (ptm) REVERT: C 3072 MET cc_start: 0.8659 (mmm) cc_final: 0.8417 (mmm) REVERT: C 3101 LEU cc_start: 0.8115 (mt) cc_final: 0.7823 (mm) REVERT: C 3104 MET cc_start: 0.8639 (ptt) cc_final: 0.7673 (pp-130) REVERT: C 3108 LEU cc_start: 0.9312 (mt) cc_final: 0.9060 (mp) REVERT: C 3111 HIS cc_start: 0.8281 (p-80) cc_final: 0.7924 (p90) REVERT: C 3117 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8418 (t80) REVERT: C 3246 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7881 (pmm) REVERT: C 3249 TRP cc_start: 0.8186 (m-10) cc_final: 0.7924 (m-10) REVERT: C 3252 HIS cc_start: 0.8391 (m90) cc_final: 0.7918 (m90) REVERT: C 3269 ASN cc_start: 0.9044 (m-40) cc_final: 0.8564 (p0) REVERT: C 3272 HIS cc_start: 0.8547 (m90) cc_final: 0.7918 (m90) REVERT: D 395 HIS cc_start: 0.7986 (m-70) cc_final: 0.7639 (m170) REVERT: D 678 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7542 (ttp) REVERT: D 995 MET cc_start: 0.8584 (mtm) cc_final: 0.8257 (mtt) REVERT: D 1050 LEU cc_start: 0.9505 (tp) cc_final: 0.9273 (pp) REVERT: D 1168 MET cc_start: 0.8693 (mmm) cc_final: 0.8310 (mmt) REVERT: D 2150 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: D 2192 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (tpt) REVERT: D 2347 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.7621 (mpt) REVERT: D 2540 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7912 (p-80) REVERT: D 2585 MET cc_start: 0.8707 (ttp) cc_final: 0.8480 (ttp) REVERT: D 2688 MET cc_start: 0.6033 (mmp) cc_final: 0.5690 (mmp) REVERT: D 2695 MET cc_start: 0.6185 (mmm) cc_final: 0.5472 (mmm) REVERT: D 2719 TYR cc_start: 0.8682 (t80) cc_final: 0.8394 (t80) REVERT: D 2724 TYR cc_start: 0.9018 (t80) cc_final: 0.8631 (t80) REVERT: D 2727 HIS cc_start: 0.9158 (t-90) cc_final: 0.8917 (m170) REVERT: D 2757 MET cc_start: 0.6858 (mtt) cc_final: 0.6655 (mpp) REVERT: D 2782 MET cc_start: 0.8036 (ptm) cc_final: 0.7546 (ptm) REVERT: D 2840 MET cc_start: 0.7795 (mmt) cc_final: 0.7332 (mmt) REVERT: D 2843 MET cc_start: 0.8680 (tpt) cc_final: 0.7827 (tpt) REVERT: D 2847 ASN cc_start: 0.9389 (t0) cc_final: 0.9186 (t0) REVERT: D 2880 LYS cc_start: 0.9252 (mppt) cc_final: 0.8858 (mppt) REVERT: D 2898 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8867 (tp) REVERT: D 2980 LEU cc_start: 0.8951 (tt) cc_final: 0.8631 (tm) REVERT: D 3003 MET cc_start: 0.8486 (ptm) cc_final: 0.8283 (ptm) REVERT: D 3007 LEU cc_start: 0.9036 (mt) cc_final: 0.8763 (mt) REVERT: D 3057 LEU cc_start: 0.9133 (tm) cc_final: 0.8803 (pp) REVERT: D 3072 MET cc_start: 0.9309 (ttt) cc_final: 0.8611 (tmm) REVERT: D 3131 TYR cc_start: 0.8808 (m-10) cc_final: 0.8590 (m-80) REVERT: D 3137 LEU cc_start: 0.9442 (mm) cc_final: 0.9174 (mp) REVERT: D 3162 PHE cc_start: 0.9050 (t80) cc_final: 0.8769 (t80) REVERT: D 3252 HIS cc_start: 0.7982 (m90) cc_final: 0.7628 (m-70) REVERT: D 3263 MET cc_start: 0.8374 (mmm) cc_final: 0.7826 (mpm) REVERT: D 3295 TRP cc_start: 0.7837 (p-90) cc_final: 0.7256 (p-90) REVERT: D 3296 MET cc_start: 0.9119 (ptp) cc_final: 0.8479 (ptp) REVERT: D 3819 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5811 (pmt) REVERT: D 4305 PHE cc_start: 0.8128 (t80) cc_final: 0.7819 (t80) REVERT: D 4306 PHE cc_start: 0.7468 (m-80) cc_final: 0.7121 (m-10) outliers start: 139 outliers final: 48 residues processed: 1010 average time/residue: 2.0018 time to fit residues: 2931.4688 Evaluate side-chains 1002 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 932 time to evaluate : 12.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3021 LEU Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2480 VAL Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 2963 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2652 LEU Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2932 TYR Chi-restraints excluded: chain C residue 3117 PHE Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 2898 ILE Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3269 ASN Chi-restraints excluded: chain D residue 3653 GLU Chi-restraints excluded: chain D residue 3819 MET Chi-restraints excluded: chain D residue 4120 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 0.9990 chunk 1504 optimal weight: 9.9990 chunk 330 optimal weight: 40.0000 chunk 980 optimal weight: 20.0000 chunk 412 optimal weight: 6.9990 chunk 1671 optimal weight: 5.9990 chunk 1387 optimal weight: 0.0970 chunk 774 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 553 optimal weight: 20.0000 chunk 877 optimal weight: 8.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 888 ASN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2316 ASN ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3269 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS B 888 ASN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 141628 Z= 0.238 Angle : 0.612 18.006 191356 Z= 0.304 Chirality : 0.040 0.324 20988 Planarity : 0.005 0.164 24588 Dihedral : 5.416 77.145 19032 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 0.89 % Allowed : 8.22 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.06), residues: 17212 helix: 1.86 (0.05), residues: 8948 sheet: 0.21 (0.13), residues: 1680 loop : -0.35 (0.08), residues: 6584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B3249 HIS 0.014 0.001 HIS B2727 PHE 0.045 0.002 PHE A2943 TYR 0.043 0.001 TYR A 931 ARG 0.017 0.000 ARG G 14 *********************** 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 1067 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 938 time to evaluate : 11.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LEU cc_start: 0.9308 (mt) cc_final: 0.8993 (pp) REVERT: A 946 LEU cc_start: 0.8435 (mt) cc_final: 0.7987 (pp) REVERT: A 995 MET cc_start: 0.8039 (mtm) cc_final: 0.7629 (mtt) REVERT: A 1050 LEU cc_start: 0.9353 (mm) cc_final: 0.9036 (tp) REVERT: A 1168 MET cc_start: 0.8317 (mmm) cc_final: 0.8101 (mmp) REVERT: A 1975 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (ppp) REVERT: A 2142 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7882 (tpp) REVERT: A 2150 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7057 (mpp) REVERT: A 2584 MET cc_start: 0.8230 (ptm) cc_final: 0.8016 (ptm) REVERT: A 2594 PHE cc_start: 0.8304 (t80) cc_final: 0.7783 (t80) REVERT: A 2689 MET cc_start: 0.5983 (tmm) cc_final: 0.5539 (mpt) REVERT: A 2723 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8692 (mmtm) REVERT: A 2724 TYR cc_start: 0.8983 (t80) cc_final: 0.8594 (t80) REVERT: A 2757 MET cc_start: 0.7165 (mtt) cc_final: 0.6722 (mpt) REVERT: A 2782 MET cc_start: 0.8413 (ptm) cc_final: 0.8086 (ppp) REVERT: A 2798 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (mpm) REVERT: A 2840 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7027 (mmt) REVERT: A 2843 MET cc_start: 0.8217 (tpt) cc_final: 0.7382 (tpt) REVERT: A 2844 MET cc_start: 0.8937 (ppp) cc_final: 0.8593 (ppp) REVERT: A 2877 LEU cc_start: 0.8820 (mt) cc_final: 0.8403 (mt) REVERT: A 2880 LYS cc_start: 0.9281 (mppt) cc_final: 0.8958 (mppt) REVERT: A 2895 PHE cc_start: 0.9166 (t80) cc_final: 0.8881 (t80) REVERT: A 2939 TYR cc_start: 0.8535 (m-80) cc_final: 0.8244 (m-80) REVERT: A 2980 LEU cc_start: 0.9038 (tt) cc_final: 0.8756 (tm) REVERT: A 3003 MET cc_start: 0.8741 (ptm) cc_final: 0.8413 (ptm) REVERT: A 3021 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 3034 HIS cc_start: 0.8380 (m90) cc_final: 0.8026 (m90) REVERT: A 3104 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (ptm) REVERT: A 3117 PHE cc_start: 0.8633 (t80) cc_final: 0.8235 (t80) REVERT: A 3131 TYR cc_start: 0.9249 (m-10) cc_final: 0.8873 (m-80) REVERT: A 3241 MET cc_start: 0.9090 (mmp) cc_final: 0.8616 (mmm) REVERT: A 3246 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7763 (pmm) REVERT: A 3250 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7842 (m100) REVERT: A 3252 HIS cc_start: 0.8305 (m90) cc_final: 0.7886 (m-70) REVERT: A 3295 TRP cc_start: 0.8131 (p-90) cc_final: 0.7706 (p-90) REVERT: A 3296 MET cc_start: 0.9180 (ptp) cc_final: 0.8719 (ptp) REVERT: A 3653 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5988 (pm20) REVERT: F 26 HIS cc_start: 0.9294 (OUTLIER) cc_final: 0.8595 (m-70) REVERT: B 940 LEU cc_start: 0.9285 (mt) cc_final: 0.8972 (pp) REVERT: B 995 MET cc_start: 0.8383 (mtm) cc_final: 0.7957 (ttt) REVERT: B 999 LEU cc_start: 0.9190 (mm) cc_final: 0.8962 (mm) REVERT: B 1050 LEU cc_start: 0.9517 (mp) cc_final: 0.9203 (tp) REVERT: B 1165 MET cc_start: 0.8395 (mpp) cc_final: 0.8161 (mtm) REVERT: B 1729 MET cc_start: 0.8013 (tpp) cc_final: 0.7675 (mmt) REVERT: B 2724 TYR cc_start: 0.8877 (t80) cc_final: 0.8526 (t80) REVERT: B 2727 HIS cc_start: 0.8697 (m-70) cc_final: 0.8324 (m170) REVERT: B 2757 MET cc_start: 0.7061 (mtt) cc_final: 0.6771 (mpt) REVERT: B 2772 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7916 (tpp80) REVERT: B 2843 MET cc_start: 0.8197 (tpt) cc_final: 0.7515 (tpt) REVERT: B 2844 MET cc_start: 0.8978 (ppp) cc_final: 0.8678 (ppp) REVERT: B 2895 PHE cc_start: 0.8806 (t80) cc_final: 0.8331 (t80) REVERT: B 2939 TYR cc_start: 0.8609 (m-80) cc_final: 0.8362 (m-80) REVERT: B 3003 MET cc_start: 0.8454 (ptm) cc_final: 0.8178 (ptm) REVERT: B 3072 MET cc_start: 0.8739 (mmm) cc_final: 0.8489 (tpp) REVERT: B 3117 PHE cc_start: 0.7996 (t80) cc_final: 0.7590 (t80) REVERT: B 3250 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.7269 (m100) REVERT: B 3252 HIS cc_start: 0.8258 (m90) cc_final: 0.7799 (m-70) REVERT: B 3273 MET cc_start: 0.9406 (mpm) cc_final: 0.8848 (mpm) REVERT: B 3295 TRP cc_start: 0.8612 (p-90) cc_final: 0.8212 (p-90) REVERT: B 3296 MET cc_start: 0.9221 (ptp) cc_final: 0.8751 (ptp) REVERT: B 3653 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: B 3819 MET cc_start: 0.5783 (pmt) cc_final: 0.5505 (pmt) REVERT: B 4048 PHE cc_start: 0.8731 (t80) cc_final: 0.8495 (t80) REVERT: B 4258 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7886 (ptm) REVERT: B 4306 PHE cc_start: 0.7603 (m-80) cc_final: 0.7251 (m-10) REVERT: C 678 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7899 (ttp) REVERT: C 874 LEU cc_start: 0.8451 (tm) cc_final: 0.8052 (tt) REVERT: C 940 LEU cc_start: 0.9228 (mt) cc_final: 0.8951 (pp) REVERT: C 964 MET cc_start: 0.1354 (OUTLIER) cc_final: 0.0798 (pmm) REVERT: C 981 MET cc_start: 0.6553 (ppp) cc_final: 0.6300 (ppp) REVERT: C 995 MET cc_start: 0.7932 (mtm) cc_final: 0.7445 (ttt) REVERT: C 999 LEU cc_start: 0.9117 (tp) cc_final: 0.8801 (mm) REVERT: C 1050 LEU cc_start: 0.9422 (mm) cc_final: 0.9166 (tp) REVERT: C 1721 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7522 (mmp) REVERT: C 2150 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7278 (mpp) REVERT: C 2688 MET cc_start: 0.6270 (mmt) cc_final: 0.5736 (mpp) REVERT: C 2689 MET cc_start: 0.5863 (tmm) cc_final: 0.5105 (mpt) REVERT: C 2757 MET cc_start: 0.7245 (mtt) cc_final: 0.6887 (mpt) REVERT: C 2782 MET cc_start: 0.8470 (ptm) cc_final: 0.8164 (ppp) REVERT: C 2828 MET cc_start: 0.8096 (mmm) cc_final: 0.7826 (mpp) REVERT: C 2840 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6494 (mmt) REVERT: C 2843 MET cc_start: 0.7991 (tpt) cc_final: 0.7183 (tpt) REVERT: C 2844 MET cc_start: 0.8918 (ppp) cc_final: 0.8585 (ppp) REVERT: C 2877 LEU cc_start: 0.8845 (mt) cc_final: 0.8459 (mt) REVERT: C 2880 LYS cc_start: 0.9294 (mppt) cc_final: 0.9039 (mppt) REVERT: C 2895 PHE cc_start: 0.9177 (t80) cc_final: 0.8844 (t80) REVERT: C 2974 TYR cc_start: 0.8300 (t80) cc_final: 0.8086 (t80) REVERT: C 2975 PHE cc_start: 0.8587 (m-10) cc_final: 0.8288 (m-10) REVERT: C 3003 MET cc_start: 0.8622 (ptm) cc_final: 0.8158 (ptm) REVERT: C 3072 MET cc_start: 0.8667 (mmm) cc_final: 0.8434 (mmm) REVERT: C 3104 MET cc_start: 0.8667 (ptt) cc_final: 0.7866 (pp-130) REVERT: C 3108 LEU cc_start: 0.9340 (mt) cc_final: 0.8803 (mp) REVERT: C 3111 HIS cc_start: 0.8256 (p-80) cc_final: 0.7645 (p90) REVERT: C 3117 PHE cc_start: 0.8855 (t80) cc_final: 0.8416 (t80) REVERT: C 3246 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7825 (pmm) REVERT: C 3249 TRP cc_start: 0.8154 (m-10) cc_final: 0.7893 (m-10) REVERT: C 3252 HIS cc_start: 0.8415 (m90) cc_final: 0.7916 (m90) REVERT: C 3269 ASN cc_start: 0.9075 (m-40) cc_final: 0.8572 (p0) REVERT: C 3272 HIS cc_start: 0.8526 (m90) cc_final: 0.7893 (m90) REVERT: D 395 HIS cc_start: 0.7937 (m-70) cc_final: 0.7594 (m-70) REVERT: D 678 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7483 (ttp) REVERT: D 995 MET cc_start: 0.8592 (mtm) cc_final: 0.8254 (mtt) REVERT: D 1168 MET cc_start: 0.8666 (mmm) cc_final: 0.8270 (mmt) REVERT: D 2150 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: D 2192 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8062 (tpt) REVERT: D 2347 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.7657 (mpt) REVERT: D 2540 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7891 (p-80) REVERT: D 2585 MET cc_start: 0.8680 (ttp) cc_final: 0.8457 (ttp) REVERT: D 2695 MET cc_start: 0.6290 (mmm) cc_final: 0.5642 (mmm) REVERT: D 2719 TYR cc_start: 0.8669 (t80) cc_final: 0.8352 (t80) REVERT: D 2724 TYR cc_start: 0.9016 (t80) cc_final: 0.8562 (t80) REVERT: D 2772 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8534 (mtm110) REVERT: D 2782 MET cc_start: 0.8045 (ptm) cc_final: 0.7555 (ptm) REVERT: D 2840 MET cc_start: 0.7773 (mmt) cc_final: 0.7422 (mmt) REVERT: D 2843 MET cc_start: 0.8644 (tpt) cc_final: 0.7805 (tpt) REVERT: D 2847 ASN cc_start: 0.9382 (t0) cc_final: 0.9181 (t0) REVERT: D 2880 LYS cc_start: 0.9257 (mppt) cc_final: 0.8867 (mppt) REVERT: D 2897 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8724 (mm-40) REVERT: D 2980 LEU cc_start: 0.8963 (tt) cc_final: 0.8637 (tm) REVERT: D 3007 LEU cc_start: 0.9065 (mt) cc_final: 0.8776 (mt) REVERT: D 3057 LEU cc_start: 0.9132 (tm) cc_final: 0.8803 (pp) REVERT: D 3072 MET cc_start: 0.9301 (ttt) cc_final: 0.8645 (tmm) REVERT: D 3131 TYR cc_start: 0.8798 (m-10) cc_final: 0.8586 (m-80) REVERT: D 3137 LEU cc_start: 0.9435 (mm) cc_final: 0.9173 (mp) REVERT: D 3162 PHE cc_start: 0.9049 (t80) cc_final: 0.8782 (t80) REVERT: D 3252 HIS cc_start: 0.7948 (m90) cc_final: 0.7602 (m-70) REVERT: D 3295 TRP cc_start: 0.7834 (p-90) cc_final: 0.7349 (p-90) REVERT: D 3296 MET cc_start: 0.9110 (ptp) cc_final: 0.8449 (ptp) REVERT: D 3819 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5766 (pmt) REVERT: D 4305 PHE cc_start: 0.8163 (t80) cc_final: 0.7864 (t80) REVERT: D 4306 PHE cc_start: 0.7508 (m-80) cc_final: 0.7153 (m-10) outliers start: 129 outliers final: 48 residues processed: 990 average time/residue: 2.0159 time to fit residues: 2905.1173 Evaluate side-chains 994 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 920 time to evaluate : 11.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3021 LEU Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3250 TRP Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1060 TYR Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3250 TRP Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1060 TYR Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2652 LEU Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2932 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 3653 GLU Chi-restraints excluded: chain D residue 3819 MET Chi-restraints excluded: chain D residue 4120 GLU Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 952 optimal weight: 7.9990 chunk 1220 optimal weight: 6.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 6.9990 chunk 933 optimal weight: 7.9990 chunk 1665 optimal weight: 0.0970 chunk 1042 optimal weight: 6.9990 chunk 1015 optimal weight: 8.9990 chunk 768 optimal weight: 20.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 930 ASN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3116 GLN ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3269 ASN ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 HIS B 57 ASN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3233 HIS ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2927 GLN ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3200 ASN ** D3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 141628 Z= 0.412 Angle : 0.668 18.337 191356 Z= 0.334 Chirality : 0.043 0.308 20988 Planarity : 0.005 0.164 24588 Dihedral : 5.496 78.390 19028 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 0.93 % Allowed : 8.53 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.06), residues: 17212 helix: 1.74 (0.05), residues: 8980 sheet: 0.10 (0.13), residues: 1560 loop : -0.42 (0.07), residues: 6672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B3249 HIS 0.012 0.001 HIS C3233 PHE 0.053 0.002 PHE B2943 TYR 0.058 0.002 TYR B3131 ARG 0.015 0.001 ARG C2772 *********************** 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 1098 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 963 time to evaluate : 11.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 LEU cc_start: 0.9345 (mt) cc_final: 0.9024 (pp) REVERT: A 946 LEU cc_start: 0.8631 (mt) cc_final: 0.8177 (pp) REVERT: A 995 MET cc_start: 0.8118 (mtm) cc_final: 0.7714 (mtt) REVERT: A 1050 LEU cc_start: 0.9366 (mm) cc_final: 0.9027 (tp) REVERT: A 2142 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7895 (tpp) REVERT: A 2150 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: A 2594 PHE cc_start: 0.8039 (t80) cc_final: 0.7617 (t80) REVERT: A 2688 MET cc_start: 0.6590 (mmt) cc_final: 0.5829 (mpp) REVERT: A 2689 MET cc_start: 0.5979 (tmm) cc_final: 0.5490 (mpt) REVERT: A 2723 LYS cc_start: 0.9256 (mtpt) cc_final: 0.8717 (mppt) REVERT: A 2724 TYR cc_start: 0.9012 (t80) cc_final: 0.8631 (t80) REVERT: A 2757 MET cc_start: 0.7205 (mtt) cc_final: 0.6745 (mpt) REVERT: A 2772 ARG cc_start: 0.8599 (mtm110) cc_final: 0.7930 (pmm-80) REVERT: A 2782 MET cc_start: 0.8501 (ptm) cc_final: 0.8185 (ppp) REVERT: A 2840 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7271 (mmt) REVERT: A 2843 MET cc_start: 0.8266 (tpt) cc_final: 0.7446 (tpt) REVERT: A 2844 MET cc_start: 0.8983 (ppp) cc_final: 0.8743 (ppp) REVERT: A 2877 LEU cc_start: 0.8808 (mt) cc_final: 0.8491 (mt) REVERT: A 2880 LYS cc_start: 0.9292 (mppt) cc_final: 0.8962 (mppt) REVERT: A 2895 PHE cc_start: 0.9147 (t80) cc_final: 0.8885 (t80) REVERT: A 2939 TYR cc_start: 0.8582 (m-80) cc_final: 0.8299 (m-80) REVERT: A 2980 LEU cc_start: 0.9103 (tt) cc_final: 0.8821 (tm) REVERT: A 2982 PHE cc_start: 0.8137 (m-80) cc_final: 0.7694 (m-10) REVERT: A 3003 MET cc_start: 0.8747 (ptm) cc_final: 0.8422 (ptm) REVERT: A 3021 LEU cc_start: 0.7122 (tp) cc_final: 0.6831 (mp) REVERT: A 3034 HIS cc_start: 0.8371 (m90) cc_final: 0.8004 (m90) REVERT: A 3104 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8469 (ptm) REVERT: A 3117 PHE cc_start: 0.8819 (t80) cc_final: 0.8398 (t80) REVERT: A 3131 TYR cc_start: 0.9253 (m-10) cc_final: 0.8903 (m-80) REVERT: A 3241 MET cc_start: 0.9123 (mmp) cc_final: 0.8673 (mmm) REVERT: A 3246 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7483 (pmm) REVERT: A 3250 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7259 (m100) REVERT: A 3252 HIS cc_start: 0.8417 (m90) cc_final: 0.7999 (m-70) REVERT: A 3269 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8375 (p0) REVERT: A 3272 HIS cc_start: 0.8469 (m90) cc_final: 0.7932 (m90) REVERT: A 3295 TRP cc_start: 0.8252 (p-90) cc_final: 0.7767 (p-90) REVERT: A 3296 MET cc_start: 0.9192 (ptp) cc_final: 0.8680 (ptp) REVERT: F 26 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8616 (m-70) REVERT: G 53 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8912 (mmtp) REVERT: B 309 MET cc_start: 0.7541 (mmp) cc_final: 0.7256 (mpp) REVERT: B 940 LEU cc_start: 0.9291 (mt) cc_final: 0.8978 (pp) REVERT: B 946 LEU cc_start: 0.8771 (mt) cc_final: 0.8314 (pp) REVERT: B 995 MET cc_start: 0.8388 (mtm) cc_final: 0.7944 (mtt) REVERT: B 1050 LEU cc_start: 0.9522 (mp) cc_final: 0.9203 (tp) REVERT: B 1165 MET cc_start: 0.8403 (mpp) cc_final: 0.7983 (mtm) REVERT: B 1729 MET cc_start: 0.8064 (tpp) cc_final: 0.7823 (mmt) REVERT: B 2688 MET cc_start: 0.6191 (mpp) cc_final: 0.5726 (mmp) REVERT: B 2689 MET cc_start: 0.5709 (tmm) cc_final: 0.5238 (mpm) REVERT: B 2695 MET cc_start: 0.4255 (mmm) cc_final: 0.3647 (mmm) REVERT: B 2724 TYR cc_start: 0.8886 (t80) cc_final: 0.8526 (t80) REVERT: B 2727 HIS cc_start: 0.8712 (m-70) cc_final: 0.8407 (m170) REVERT: B 2757 MET cc_start: 0.7038 (mtt) cc_final: 0.6704 (mpt) REVERT: B 2772 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7913 (tpp80) REVERT: B 2840 MET cc_start: 0.7614 (mmt) cc_final: 0.7198 (mmt) REVERT: B 2843 MET cc_start: 0.8255 (tpt) cc_final: 0.7419 (tpt) REVERT: B 2844 MET cc_start: 0.9039 (ppp) cc_final: 0.8821 (ppp) REVERT: B 2847 ASN cc_start: 0.8732 (t0) cc_final: 0.8525 (t0) REVERT: B 2895 PHE cc_start: 0.8821 (t80) cc_final: 0.8327 (t80) REVERT: B 2939 TYR cc_start: 0.8655 (m-80) cc_final: 0.8401 (m-80) REVERT: B 3072 MET cc_start: 0.8694 (mmm) cc_final: 0.8444 (tpp) REVERT: B 3117 PHE cc_start: 0.8208 (t80) cc_final: 0.7702 (t80) REVERT: B 3250 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.7484 (m100) REVERT: B 3252 HIS cc_start: 0.8321 (m90) cc_final: 0.7869 (m-70) REVERT: B 3273 MET cc_start: 0.9457 (mpm) cc_final: 0.8941 (mpm) REVERT: B 3295 TRP cc_start: 0.8655 (p-90) cc_final: 0.8255 (p-90) REVERT: B 3296 MET cc_start: 0.9228 (ptp) cc_final: 0.8678 (ptp) REVERT: B 3653 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: B 3819 MET cc_start: 0.5902 (pmt) cc_final: 0.5640 (pmt) REVERT: B 4048 PHE cc_start: 0.8740 (t80) cc_final: 0.8529 (t80) REVERT: B 4258 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (ptm) REVERT: B 4306 PHE cc_start: 0.7622 (m-80) cc_final: 0.7250 (m-10) REVERT: C 678 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (ttp) REVERT: C 946 LEU cc_start: 0.8489 (mt) cc_final: 0.7996 (pp) REVERT: C 995 MET cc_start: 0.8033 (mtm) cc_final: 0.7662 (mtt) REVERT: C 999 LEU cc_start: 0.9147 (tp) cc_final: 0.8822 (mm) REVERT: C 1050 LEU cc_start: 0.9435 (mm) cc_final: 0.9181 (tp) REVERT: C 1721 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7571 (mmp) REVERT: C 2150 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: C 2594 PHE cc_start: 0.8092 (t80) cc_final: 0.7634 (t80) REVERT: C 2662 PHE cc_start: 0.8340 (m-10) cc_final: 0.8064 (m-10) REVERT: C 2681 MET cc_start: 0.7550 (mmm) cc_final: 0.7315 (tmm) REVERT: C 2688 MET cc_start: 0.6267 (mmt) cc_final: 0.5726 (mpp) REVERT: C 2689 MET cc_start: 0.5967 (tmm) cc_final: 0.5156 (mpt) REVERT: C 2757 MET cc_start: 0.7212 (mtt) cc_final: 0.6884 (mpt) REVERT: C 2772 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7994 (mmm160) REVERT: C 2782 MET cc_start: 0.8549 (ptm) cc_final: 0.8324 (ppp) REVERT: C 2828 MET cc_start: 0.8115 (mmm) cc_final: 0.7850 (mpp) REVERT: C 2840 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6630 (mmt) REVERT: C 2843 MET cc_start: 0.8052 (tpt) cc_final: 0.7231 (tpt) REVERT: C 2844 MET cc_start: 0.8982 (ppp) cc_final: 0.8658 (ppp) REVERT: C 2877 LEU cc_start: 0.8832 (mt) cc_final: 0.8448 (mt) REVERT: C 2880 LYS cc_start: 0.9312 (mppt) cc_final: 0.9045 (mppt) REVERT: C 2899 ASN cc_start: 0.8644 (m-40) cc_final: 0.7815 (t0) REVERT: C 2939 TYR cc_start: 0.8862 (m-10) cc_final: 0.8595 (m-80) REVERT: C 2975 PHE cc_start: 0.8608 (m-10) cc_final: 0.8297 (m-10) REVERT: C 3003 MET cc_start: 0.8686 (ptm) cc_final: 0.8228 (ptm) REVERT: C 3072 MET cc_start: 0.8648 (mmm) cc_final: 0.8435 (mmm) REVERT: C 3104 MET cc_start: 0.8841 (ptt) cc_final: 0.8585 (ptt) REVERT: C 3108 LEU cc_start: 0.9343 (mt) cc_final: 0.8807 (mp) REVERT: C 3111 HIS cc_start: 0.8306 (p-80) cc_final: 0.7694 (p90) REVERT: C 3117 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8598 (t80) REVERT: C 3246 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7847 (pmm) REVERT: C 3249 TRP cc_start: 0.8292 (m-10) cc_final: 0.7986 (m-10) REVERT: C 3252 HIS cc_start: 0.8392 (m90) cc_final: 0.7908 (m90) REVERT: C 3269 ASN cc_start: 0.9095 (m-40) cc_final: 0.8591 (p0) REVERT: C 3272 HIS cc_start: 0.8517 (m90) cc_final: 0.7696 (m90) REVERT: C 4258 MET cc_start: 0.8220 (ptm) cc_final: 0.8015 (ptp) REVERT: D 395 HIS cc_start: 0.7944 (m-70) cc_final: 0.7608 (m-70) REVERT: D 995 MET cc_start: 0.8622 (mtm) cc_final: 0.8376 (mtt) REVERT: D 1165 MET cc_start: 0.8132 (mtp) cc_final: 0.7801 (mtp) REVERT: D 1168 MET cc_start: 0.8610 (mmm) cc_final: 0.8215 (mmt) REVERT: D 2150 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: D 2192 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8078 (tpt) REVERT: D 2347 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7643 (mpt) REVERT: D 2540 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (p-80) REVERT: D 2585 MET cc_start: 0.8687 (ttp) cc_final: 0.8476 (ttp) REVERT: D 2649 PHE cc_start: 0.8787 (t80) cc_final: 0.8513 (t80) REVERT: D 2652 LEU cc_start: 0.9091 (tp) cc_final: 0.8663 (tm) REVERT: D 2695 MET cc_start: 0.6464 (mmm) cc_final: 0.5855 (mmm) REVERT: D 2719 TYR cc_start: 0.8720 (t80) cc_final: 0.8369 (t80) REVERT: D 2724 TYR cc_start: 0.9032 (t80) cc_final: 0.8630 (t80) REVERT: D 2757 MET cc_start: 0.6346 (mpp) cc_final: 0.5645 (mmm) REVERT: D 2782 MET cc_start: 0.8151 (ptm) cc_final: 0.7649 (ptm) REVERT: D 2798 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7379 (mpm) REVERT: D 2840 MET cc_start: 0.7870 (mmt) cc_final: 0.7446 (mmt) REVERT: D 2843 MET cc_start: 0.8628 (tpt) cc_final: 0.7791 (tpt) REVERT: D 2847 ASN cc_start: 0.9384 (t0) cc_final: 0.9051 (t0) REVERT: D 2880 LYS cc_start: 0.9273 (mppt) cc_final: 0.8866 (mppt) REVERT: D 2980 LEU cc_start: 0.9002 (tt) cc_final: 0.8677 (tm) REVERT: D 3007 LEU cc_start: 0.9084 (mt) cc_final: 0.8805 (mp) REVERT: D 3021 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7009 (mp) REVERT: D 3057 LEU cc_start: 0.9150 (tm) cc_final: 0.8833 (pp) REVERT: D 3072 MET cc_start: 0.9304 (ttt) cc_final: 0.8686 (tmm) REVERT: D 3131 TYR cc_start: 0.8789 (m-10) cc_final: 0.8588 (m-80) REVERT: D 3137 LEU cc_start: 0.9430 (mm) cc_final: 0.9188 (mp) REVERT: D 3162 PHE cc_start: 0.9065 (t80) cc_final: 0.8814 (t80) REVERT: D 3252 HIS cc_start: 0.8165 (m90) cc_final: 0.7839 (m-70) REVERT: D 3263 MET cc_start: 0.8376 (mmm) cc_final: 0.7735 (mpm) REVERT: D 3295 TRP cc_start: 0.7928 (p-90) cc_final: 0.7483 (p-90) REVERT: D 3296 MET cc_start: 0.9157 (ptp) cc_final: 0.8435 (ptp) REVERT: D 4306 PHE cc_start: 0.7504 (m-80) cc_final: 0.7125 (m-10) outliers start: 135 outliers final: 58 residues processed: 1019 average time/residue: 2.0287 time to fit residues: 3008.2735 Evaluate side-chains 1023 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 942 time to evaluate : 11.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3250 TRP Chi-restraints excluded: chain A residue 3269 ASN Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1060 TYR Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2134 MET Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3250 TRP Chi-restraints excluded: chain B residue 3653 GLU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1060 TYR Chi-restraints excluded: chain C residue 1564 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2775 ILE Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 2932 TYR Chi-restraints excluded: chain C residue 2963 PHE Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3117 PHE Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2798 MET Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3245 TYR Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 3.9990 chunk 665 optimal weight: 7.9990 chunk 994 optimal weight: 2.9990 chunk 501 optimal weight: 20.0000 chunk 327 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 1058 optimal weight: 5.9990 chunk 1134 optimal weight: 30.0000 chunk 823 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 1309 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2937 HIS ** A3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3114 GLN A3116 GLN ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3179 ASN A3233 HIS A3269 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 HIS B 57 ASN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3114 GLN ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS B3269 ASN ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2316 ASN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3116 GLN ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 141628 Z= 0.181 Angle : 0.624 19.003 191356 Z= 0.307 Chirality : 0.040 0.378 20988 Planarity : 0.004 0.127 24588 Dihedral : 5.342 77.707 19028 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 0.76 % Allowed : 8.99 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.06), residues: 17212 helix: 1.87 (0.05), residues: 8968 sheet: 0.14 (0.13), residues: 1704 loop : -0.34 (0.08), residues: 6540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP C3250 HIS 0.014 0.001 HIS D3233 PHE 0.092 0.001 PHE C2963 TYR 0.044 0.001 TYR D2939 ARG 0.013 0.000 ARG C4046 *********************** 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 1053 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 943 time to evaluate : 11.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: A 940 LEU cc_start: 0.9304 (mt) cc_final: 0.8993 (pp) REVERT: A 946 LEU cc_start: 0.8565 (mt) cc_final: 0.8126 (pp) REVERT: A 995 MET cc_start: 0.8080 (mtm) cc_final: 0.7709 (mtt) REVERT: A 1050 LEU cc_start: 0.9339 (mm) cc_final: 0.8998 (tp) REVERT: A 2142 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: A 2688 MET cc_start: 0.6564 (mmt) cc_final: 0.5826 (mpp) REVERT: A 2689 MET cc_start: 0.5904 (tmm) cc_final: 0.5472 (mpt) REVERT: A 2723 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8470 (tptt) REVERT: A 2724 TYR cc_start: 0.8970 (t80) cc_final: 0.8616 (t80) REVERT: A 2757 MET cc_start: 0.6944 (mtt) cc_final: 0.6677 (mpt) REVERT: A 2782 MET cc_start: 0.8501 (ptm) cc_final: 0.8164 (ppp) REVERT: A 2840 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7330 (mmt) REVERT: A 2843 MET cc_start: 0.8197 (tpt) cc_final: 0.7402 (tpt) REVERT: A 2844 MET cc_start: 0.8989 (ppp) cc_final: 0.8714 (ppp) REVERT: A 2874 TYR cc_start: 0.7106 (t80) cc_final: 0.6878 (t80) REVERT: A 2877 LEU cc_start: 0.8804 (mt) cc_final: 0.8466 (mt) REVERT: A 2880 LYS cc_start: 0.9291 (mppt) cc_final: 0.8956 (mppt) REVERT: A 2895 PHE cc_start: 0.9012 (t80) cc_final: 0.8251 (t80) REVERT: A 2939 TYR cc_start: 0.8545 (m-80) cc_final: 0.8242 (m-80) REVERT: A 2980 LEU cc_start: 0.9055 (tt) cc_final: 0.8766 (tm) REVERT: A 3003 MET cc_start: 0.8704 (ptm) cc_final: 0.8484 (ptm) REVERT: A 3021 LEU cc_start: 0.7063 (tp) cc_final: 0.6807 (mp) REVERT: A 3034 HIS cc_start: 0.8303 (m90) cc_final: 0.7948 (m90) REVERT: A 3072 MET cc_start: 0.8324 (ptm) cc_final: 0.8103 (ptp) REVERT: A 3104 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8464 (ptm) REVERT: A 3117 PHE cc_start: 0.8738 (t80) cc_final: 0.8383 (t80) REVERT: A 3131 TYR cc_start: 0.9242 (m-10) cc_final: 0.8889 (m-80) REVERT: A 3241 MET cc_start: 0.9096 (mmp) cc_final: 0.8641 (mmm) REVERT: A 3246 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7551 (pmm) REVERT: A 3250 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7125 (m100) REVERT: A 3252 HIS cc_start: 0.8334 (m90) cc_final: 0.7909 (m-70) REVERT: A 3263 MET cc_start: 0.7389 (tpt) cc_final: 0.7089 (mpm) REVERT: A 3269 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 3272 HIS cc_start: 0.8436 (m90) cc_final: 0.8083 (m90) REVERT: A 3295 TRP cc_start: 0.8222 (p-90) cc_final: 0.7919 (p-90) REVERT: A 3296 MET cc_start: 0.9161 (ptp) cc_final: 0.8795 (ptp) REVERT: F 26 HIS cc_start: 0.9270 (OUTLIER) cc_final: 0.8572 (m-70) REVERT: B 309 MET cc_start: 0.7491 (mmp) cc_final: 0.7250 (mpp) REVERT: B 940 LEU cc_start: 0.9257 (mt) cc_final: 0.8939 (pp) REVERT: B 995 MET cc_start: 0.8379 (mtm) cc_final: 0.7988 (ttt) REVERT: B 1050 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9195 (tp) REVERT: B 1113 MET cc_start: 0.8721 (mtm) cc_final: 0.8449 (mtp) REVERT: B 1165 MET cc_start: 0.8326 (mpp) cc_final: 0.8105 (mtm) REVERT: B 1729 MET cc_start: 0.8034 (tpp) cc_final: 0.7825 (mmt) REVERT: B 2688 MET cc_start: 0.6149 (mpp) cc_final: 0.5607 (mmp) REVERT: B 2689 MET cc_start: 0.5490 (tmm) cc_final: 0.5019 (mpm) REVERT: B 2724 TYR cc_start: 0.8847 (t80) cc_final: 0.8403 (t80) REVERT: B 2757 MET cc_start: 0.6793 (mtt) cc_final: 0.6538 (mpt) REVERT: B 2772 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7907 (tpp80) REVERT: B 2840 MET cc_start: 0.7628 (mmt) cc_final: 0.7319 (mmt) REVERT: B 2843 MET cc_start: 0.8285 (tpt) cc_final: 0.7499 (tpt) REVERT: B 2844 MET cc_start: 0.9134 (ppp) cc_final: 0.8910 (ppp) REVERT: B 2847 ASN cc_start: 0.8822 (t0) cc_final: 0.8554 (t0) REVERT: B 2884 LYS cc_start: 0.9075 (pptt) cc_final: 0.8863 (tmmt) REVERT: B 2939 TYR cc_start: 0.8638 (m-80) cc_final: 0.8362 (m-80) REVERT: B 3036 LEU cc_start: 0.9296 (mp) cc_final: 0.8662 (tt) REVERT: B 3072 MET cc_start: 0.8665 (mmm) cc_final: 0.8421 (tpp) REVERT: B 3117 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 3250 TRP cc_start: 0.8063 (OUTLIER) cc_final: 0.7405 (m100) REVERT: B 3252 HIS cc_start: 0.8228 (m90) cc_final: 0.7787 (m-70) REVERT: B 3273 MET cc_start: 0.9441 (mpm) cc_final: 0.8963 (mpm) REVERT: B 3295 TRP cc_start: 0.8613 (p-90) cc_final: 0.8218 (p-90) REVERT: B 3296 MET cc_start: 0.9202 (ptp) cc_final: 0.8868 (ptp) REVERT: B 3819 MET cc_start: 0.5704 (pmt) cc_final: 0.5449 (pmt) REVERT: B 4048 PHE cc_start: 0.8736 (t80) cc_final: 0.8504 (t80) REVERT: B 4258 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7883 (ptm) REVERT: B 4306 PHE cc_start: 0.7616 (m-80) cc_final: 0.7262 (m-10) REVERT: C 678 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: C 940 LEU cc_start: 0.9261 (mt) cc_final: 0.8868 (pp) REVERT: C 946 LEU cc_start: 0.8459 (mt) cc_final: 0.7975 (pp) REVERT: C 964 MET cc_start: 0.1194 (OUTLIER) cc_final: 0.0647 (pmm) REVERT: C 981 MET cc_start: 0.6373 (ppp) cc_final: 0.6105 (ppp) REVERT: C 995 MET cc_start: 0.7972 (mtm) cc_final: 0.7530 (mtt) REVERT: C 999 LEU cc_start: 0.9092 (tp) cc_final: 0.8806 (mm) REVERT: C 1050 LEU cc_start: 0.9422 (mm) cc_final: 0.9170 (tp) REVERT: C 1721 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7507 (mmp) REVERT: C 2150 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: C 2456 MET cc_start: 0.8316 (mmm) cc_final: 0.8035 (mmm) REVERT: C 2584 MET cc_start: 0.8511 (ptm) cc_final: 0.8269 (ptm) REVERT: C 2594 PHE cc_start: 0.8125 (t80) cc_final: 0.7776 (t80) REVERT: C 2688 MET cc_start: 0.6220 (mmt) cc_final: 0.5705 (mpp) REVERT: C 2689 MET cc_start: 0.5881 (tmm) cc_final: 0.5136 (mpt) REVERT: C 2723 LYS cc_start: 0.9386 (mtpt) cc_final: 0.8962 (mmtm) REVERT: C 2757 MET cc_start: 0.7040 (mtt) cc_final: 0.6762 (mpt) REVERT: C 2772 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7907 (mmm160) REVERT: C 2782 MET cc_start: 0.8567 (ptm) cc_final: 0.8310 (ppp) REVERT: C 2828 MET cc_start: 0.8007 (mmm) cc_final: 0.7779 (mpp) REVERT: C 2840 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6736 (mmt) REVERT: C 2843 MET cc_start: 0.8035 (tpt) cc_final: 0.7217 (tpt) REVERT: C 2844 MET cc_start: 0.8967 (ppp) cc_final: 0.8620 (ppp) REVERT: C 2877 LEU cc_start: 0.8820 (mt) cc_final: 0.8425 (mt) REVERT: C 2880 LYS cc_start: 0.9310 (mppt) cc_final: 0.9045 (mppt) REVERT: C 2895 PHE cc_start: 0.9108 (t80) cc_final: 0.8624 (t80) REVERT: C 2899 ASN cc_start: 0.8633 (m-40) cc_final: 0.8042 (m110) REVERT: C 2975 PHE cc_start: 0.8531 (m-10) cc_final: 0.8274 (m-10) REVERT: C 3003 MET cc_start: 0.8694 (ptm) cc_final: 0.8174 (ptm) REVERT: C 3021 LEU cc_start: 0.7091 (tp) cc_final: 0.6752 (mt) REVERT: C 3108 LEU cc_start: 0.9337 (mt) cc_final: 0.8666 (mt) REVERT: C 3111 HIS cc_start: 0.8243 (p-80) cc_final: 0.7593 (p90) REVERT: C 3117 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8542 (t80) REVERT: C 3246 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7831 (pmm) REVERT: C 3249 TRP cc_start: 0.8127 (m-10) cc_final: 0.7839 (m-10) REVERT: C 3252 HIS cc_start: 0.8291 (m90) cc_final: 0.7800 (m90) REVERT: C 3269 ASN cc_start: 0.9075 (m-40) cc_final: 0.8567 (p0) REVERT: C 3272 HIS cc_start: 0.8471 (m90) cc_final: 0.7668 (m90) REVERT: D 395 HIS cc_start: 0.7909 (m-70) cc_final: 0.7591 (m-70) REVERT: D 678 MET cc_start: 0.8098 (tpp) cc_final: 0.7628 (ttp) REVERT: D 1168 MET cc_start: 0.8599 (mmm) cc_final: 0.8312 (mmp) REVERT: D 1975 MET cc_start: 0.8225 (pp-130) cc_final: 0.7963 (ppp) REVERT: D 2150 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7076 (mpp) REVERT: D 2192 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8049 (tpt) REVERT: D 2347 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7760 (mpt) REVERT: D 2540 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7991 (p-80) REVERT: D 2585 MET cc_start: 0.8652 (ttp) cc_final: 0.8432 (ttp) REVERT: D 2652 LEU cc_start: 0.9064 (tp) cc_final: 0.8614 (tm) REVERT: D 2695 MET cc_start: 0.6557 (mmm) cc_final: 0.6053 (mmm) REVERT: D 2724 TYR cc_start: 0.8983 (t80) cc_final: 0.8640 (t80) REVERT: D 2782 MET cc_start: 0.8127 (ptm) cc_final: 0.7587 (ptm) REVERT: D 2840 MET cc_start: 0.7740 (mmt) cc_final: 0.7343 (mmt) REVERT: D 2843 MET cc_start: 0.8604 (tpt) cc_final: 0.7687 (tpt) REVERT: D 2847 ASN cc_start: 0.9364 (t0) cc_final: 0.9160 (t0) REVERT: D 2880 LYS cc_start: 0.9267 (mppt) cc_final: 0.8848 (mppt) REVERT: D 2897 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8746 (mm-40) REVERT: D 2980 LEU cc_start: 0.8980 (tt) cc_final: 0.8651 (tm) REVERT: D 3003 MET cc_start: 0.8610 (ptm) cc_final: 0.7865 (ptp) REVERT: D 3007 LEU cc_start: 0.9086 (mt) cc_final: 0.8759 (mm) REVERT: D 3021 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6912 (mp) REVERT: D 3057 LEU cc_start: 0.9131 (tm) cc_final: 0.8785 (pp) REVERT: D 3072 MET cc_start: 0.9273 (ttt) cc_final: 0.8713 (tmm) REVERT: D 3131 TYR cc_start: 0.8772 (m-10) cc_final: 0.8552 (m-80) REVERT: D 3137 LEU cc_start: 0.9421 (mm) cc_final: 0.9191 (mp) REVERT: D 3162 PHE cc_start: 0.9058 (t80) cc_final: 0.8804 (t80) REVERT: D 3246 MET cc_start: 0.7747 (mmt) cc_final: 0.7441 (mpt) REVERT: D 3252 HIS cc_start: 0.8107 (m90) cc_final: 0.7766 (m-70) REVERT: D 3263 MET cc_start: 0.8346 (mmm) cc_final: 0.7718 (mpm) REVERT: D 3295 TRP cc_start: 0.7893 (p-90) cc_final: 0.7306 (p-90) REVERT: D 3296 MET cc_start: 0.9106 (ptp) cc_final: 0.8357 (ptp) REVERT: D 3719 MET cc_start: 0.7708 (tpp) cc_final: 0.7504 (tpt) REVERT: D 4302 PHE cc_start: 0.7920 (m-10) cc_final: 0.7539 (m-10) REVERT: D 4306 PHE cc_start: 0.7492 (m-80) cc_final: 0.7124 (m-10) outliers start: 110 outliers final: 43 residues processed: 992 average time/residue: 2.0168 time to fit residues: 2912.3020 Evaluate side-chains 994 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 927 time to evaluate : 11.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 2963 PHE Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3233 HIS Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3250 TRP Chi-restraints excluded: chain A residue 3269 ASN Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1060 TYR Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3117 PHE Chi-restraints excluded: chain B residue 3233 HIS Chi-restraints excluded: chain B residue 3250 TRP Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2775 ILE Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3117 PHE Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 8.9990 chunk 1595 optimal weight: 4.9990 chunk 1455 optimal weight: 3.9990 chunk 1552 optimal weight: 20.0000 chunk 934 optimal weight: 10.0000 chunk 676 optimal weight: 0.0040 chunk 1218 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 1402 optimal weight: 20.0000 chunk 1467 optimal weight: 0.0050 chunk 1546 optimal weight: 40.0000 overall best weight: 3.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3116 GLN ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3269 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3269 ASN ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2727 HIS ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3233 HIS D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 141628 Z= 0.280 Angle : 0.647 20.656 191356 Z= 0.318 Chirality : 0.041 0.447 20988 Planarity : 0.005 0.126 24588 Dihedral : 5.326 78.316 19028 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 0.68 % Allowed : 9.15 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.06), residues: 17212 helix: 1.85 (0.05), residues: 8972 sheet: 0.13 (0.13), residues: 1608 loop : -0.36 (0.08), residues: 6632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C3250 HIS 0.016 0.001 HIS A3233 PHE 0.054 0.002 PHE D2943 TYR 0.051 0.001 TYR C 931 ARG 0.015 0.000 ARG B4046 *********************** 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 1043 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 945 time to evaluate : 13.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: A 241 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7219 (pmm) REVERT: A 678 MET cc_start: 0.8175 (tpp) cc_final: 0.7797 (ttp) REVERT: A 930 ASN cc_start: 0.8815 (m110) cc_final: 0.8547 (m-40) REVERT: A 940 LEU cc_start: 0.9317 (mt) cc_final: 0.8988 (pp) REVERT: A 946 LEU cc_start: 0.8629 (mt) cc_final: 0.8199 (pp) REVERT: A 995 MET cc_start: 0.8120 (mtm) cc_final: 0.7736 (mtt) REVERT: A 1050 LEU cc_start: 0.9333 (mm) cc_final: 0.9011 (tp) REVERT: A 2142 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7917 (tpp) REVERT: A 2688 MET cc_start: 0.6590 (mmt) cc_final: 0.5838 (mpp) REVERT: A 2689 MET cc_start: 0.5867 (tmm) cc_final: 0.5485 (mpt) REVERT: A 2723 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8296 (mppt) REVERT: A 2724 TYR cc_start: 0.8968 (t80) cc_final: 0.8713 (t80) REVERT: A 2727 HIS cc_start: 0.9406 (t-90) cc_final: 0.9136 (m-70) REVERT: A 2757 MET cc_start: 0.6947 (mtt) cc_final: 0.6633 (mpt) REVERT: A 2782 MET cc_start: 0.8518 (ptm) cc_final: 0.8187 (ppp) REVERT: A 2840 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7380 (mmt) REVERT: A 2843 MET cc_start: 0.8205 (tpt) cc_final: 0.7411 (tpt) REVERT: A 2844 MET cc_start: 0.8999 (ppp) cc_final: 0.8721 (ppp) REVERT: A 2877 LEU cc_start: 0.8808 (mt) cc_final: 0.8485 (mt) REVERT: A 2880 LYS cc_start: 0.9307 (mppt) cc_final: 0.8979 (mppt) REVERT: A 2895 PHE cc_start: 0.8991 (t80) cc_final: 0.7878 (t80) REVERT: A 2939 TYR cc_start: 0.8578 (m-80) cc_final: 0.8292 (m-80) REVERT: A 2980 LEU cc_start: 0.9075 (tt) cc_final: 0.8790 (tm) REVERT: A 2982 PHE cc_start: 0.8078 (m-80) cc_final: 0.7652 (m-10) REVERT: A 3003 MET cc_start: 0.8775 (ptm) cc_final: 0.8443 (ptm) REVERT: A 3021 LEU cc_start: 0.7075 (tp) cc_final: 0.6824 (mp) REVERT: A 3034 HIS cc_start: 0.8308 (m90) cc_final: 0.7931 (m90) REVERT: A 3104 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8468 (ptm) REVERT: A 3117 PHE cc_start: 0.8780 (t80) cc_final: 0.8431 (t80) REVERT: A 3131 TYR cc_start: 0.9247 (m-10) cc_final: 0.8898 (m-80) REVERT: A 3241 MET cc_start: 0.9115 (mmp) cc_final: 0.8655 (mmm) REVERT: A 3246 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7490 (pmm) REVERT: A 3250 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.7157 (m100) REVERT: A 3252 HIS cc_start: 0.8364 (m90) cc_final: 0.7937 (m-70) REVERT: A 3269 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 3272 HIS cc_start: 0.8433 (m90) cc_final: 0.7731 (m90) REVERT: A 3295 TRP cc_start: 0.8258 (p-90) cc_final: 0.7901 (p-90) REVERT: A 3296 MET cc_start: 0.9170 (ptp) cc_final: 0.8774 (ptp) REVERT: F 19 LYS cc_start: 0.9065 (mmpt) cc_final: 0.8722 (mmmm) REVERT: F 26 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.8596 (m-70) REVERT: B 309 MET cc_start: 0.7484 (mmp) cc_final: 0.7219 (mpp) REVERT: B 940 LEU cc_start: 0.9252 (mt) cc_final: 0.8937 (pp) REVERT: B 946 LEU cc_start: 0.8851 (mt) cc_final: 0.8423 (pp) REVERT: B 995 MET cc_start: 0.8390 (mtm) cc_final: 0.7947 (mtt) REVERT: B 1050 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9207 (tp) REVERT: B 1113 MET cc_start: 0.8814 (mtm) cc_final: 0.8595 (mtp) REVERT: B 1165 MET cc_start: 0.8365 (mpp) cc_final: 0.8044 (mtm) REVERT: B 2688 MET cc_start: 0.6186 (mpp) cc_final: 0.5757 (mmp) REVERT: B 2689 MET cc_start: 0.5507 (tmm) cc_final: 0.5105 (mpm) REVERT: B 2695 MET cc_start: 0.4002 (mmm) cc_final: 0.3513 (mmm) REVERT: B 2724 TYR cc_start: 0.8792 (t80) cc_final: 0.7817 (t80) REVERT: B 2730 ASP cc_start: 0.9266 (m-30) cc_final: 0.8870 (t0) REVERT: B 2754 GLN cc_start: 0.9375 (tp-100) cc_final: 0.8577 (pp30) REVERT: B 2757 MET cc_start: 0.6882 (mtt) cc_final: 0.6418 (mmp) REVERT: B 2772 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7913 (tpp80) REVERT: B 2840 MET cc_start: 0.7692 (mmt) cc_final: 0.7365 (mmt) REVERT: B 2843 MET cc_start: 0.8311 (tpt) cc_final: 0.7545 (tpt) REVERT: B 2844 MET cc_start: 0.9169 (ppp) cc_final: 0.8915 (ppp) REVERT: B 2847 ASN cc_start: 0.8935 (t0) cc_final: 0.8680 (t0) REVERT: B 2884 LYS cc_start: 0.9081 (pptt) cc_final: 0.8871 (tmmt) REVERT: B 2895 PHE cc_start: 0.8995 (t80) cc_final: 0.7416 (t80) REVERT: B 2939 TYR cc_start: 0.8654 (m-80) cc_final: 0.8341 (m-80) REVERT: B 3072 MET cc_start: 0.8651 (mmm) cc_final: 0.8423 (tpp) REVERT: B 3117 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7672 (t80) REVERT: B 3250 TRP cc_start: 0.8120 (OUTLIER) cc_final: 0.7455 (m100) REVERT: B 3252 HIS cc_start: 0.8243 (m90) cc_final: 0.7782 (m-70) REVERT: B 3273 MET cc_start: 0.9457 (mpm) cc_final: 0.9018 (mpm) REVERT: B 3295 TRP cc_start: 0.8613 (p-90) cc_final: 0.8219 (p-90) REVERT: B 3296 MET cc_start: 0.9202 (ptp) cc_final: 0.8873 (ptp) REVERT: B 3819 MET cc_start: 0.5823 (pmt) cc_final: 0.5585 (pmt) REVERT: B 4048 PHE cc_start: 0.8734 (t80) cc_final: 0.8516 (t80) REVERT: B 4258 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (ptm) REVERT: B 4306 PHE cc_start: 0.7621 (m-80) cc_final: 0.7267 (m-10) REVERT: C 678 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7876 (ttp) REVERT: C 940 LEU cc_start: 0.9303 (mt) cc_final: 0.8916 (pp) REVERT: C 946 LEU cc_start: 0.8505 (mt) cc_final: 0.8008 (pp) REVERT: C 964 MET cc_start: 0.1276 (OUTLIER) cc_final: 0.0691 (pmm) REVERT: C 981 MET cc_start: 0.6437 (ppp) cc_final: 0.6234 (ppp) REVERT: C 995 MET cc_start: 0.8009 (mtm) cc_final: 0.7550 (mtt) REVERT: C 999 LEU cc_start: 0.9106 (tp) cc_final: 0.8833 (mm) REVERT: C 1050 LEU cc_start: 0.9423 (mm) cc_final: 0.9167 (tp) REVERT: C 1721 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7535 (mmp) REVERT: C 2150 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7205 (mpp) REVERT: C 2456 MET cc_start: 0.8325 (mmm) cc_final: 0.8090 (mmm) REVERT: C 2584 MET cc_start: 0.8495 (ptm) cc_final: 0.8255 (ptm) REVERT: C 2688 MET cc_start: 0.6301 (mmt) cc_final: 0.5803 (mpp) REVERT: C 2689 MET cc_start: 0.5919 (tmm) cc_final: 0.5202 (mpt) REVERT: C 2723 LYS cc_start: 0.9393 (mtpt) cc_final: 0.8988 (mmtm) REVERT: C 2757 MET cc_start: 0.6984 (mtt) cc_final: 0.6755 (mpt) REVERT: C 2782 MET cc_start: 0.8602 (ptm) cc_final: 0.8363 (ppp) REVERT: C 2828 MET cc_start: 0.7947 (mmm) cc_final: 0.7703 (mpp) REVERT: C 2840 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6789 (mmt) REVERT: C 2843 MET cc_start: 0.8098 (tpt) cc_final: 0.7287 (tpt) REVERT: C 2844 MET cc_start: 0.8993 (ppp) cc_final: 0.8667 (ppp) REVERT: C 2877 LEU cc_start: 0.8818 (mt) cc_final: 0.8419 (mt) REVERT: C 2880 LYS cc_start: 0.9315 (mppt) cc_final: 0.9039 (mppt) REVERT: C 2895 PHE cc_start: 0.9154 (t80) cc_final: 0.8662 (t80) REVERT: C 2899 ASN cc_start: 0.8651 (m-40) cc_final: 0.8023 (m110) REVERT: C 2939 TYR cc_start: 0.8849 (m-10) cc_final: 0.8543 (m-80) REVERT: C 2975 PHE cc_start: 0.8553 (m-10) cc_final: 0.8278 (m-10) REVERT: C 3003 MET cc_start: 0.8724 (ptm) cc_final: 0.8194 (ptm) REVERT: C 3021 LEU cc_start: 0.7105 (tp) cc_final: 0.6746 (mp) REVERT: C 3108 LEU cc_start: 0.9334 (mt) cc_final: 0.8659 (mt) REVERT: C 3111 HIS cc_start: 0.8257 (p-80) cc_final: 0.7610 (p90) REVERT: C 3117 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8566 (t80) REVERT: C 3246 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7722 (pmm) REVERT: C 3249 TRP cc_start: 0.8212 (m-10) cc_final: 0.7964 (m-10) REVERT: C 3250 TRP cc_start: 0.8244 (m100) cc_final: 0.7208 (m100) REVERT: C 3252 HIS cc_start: 0.8324 (m90) cc_final: 0.7815 (m90) REVERT: C 3269 ASN cc_start: 0.9136 (m-40) cc_final: 0.8543 (p0) REVERT: C 3272 HIS cc_start: 0.8496 (m90) cc_final: 0.7672 (m90) REVERT: D 395 HIS cc_start: 0.7919 (m-70) cc_final: 0.7607 (m-70) REVERT: D 678 MET cc_start: 0.8142 (tpp) cc_final: 0.7816 (ttp) REVERT: D 1168 MET cc_start: 0.8583 (mmm) cc_final: 0.8294 (mmp) REVERT: D 1975 MET cc_start: 0.8236 (pp-130) cc_final: 0.7966 (ppp) REVERT: D 2150 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: D 2192 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8012 (tpt) REVERT: D 2347 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7759 (mpt) REVERT: D 2540 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7975 (p-80) REVERT: D 2585 MET cc_start: 0.8673 (ttp) cc_final: 0.8470 (ttp) REVERT: D 2695 MET cc_start: 0.6705 (mmm) cc_final: 0.6056 (mmm) REVERT: D 2724 TYR cc_start: 0.8995 (t80) cc_final: 0.8602 (t80) REVERT: D 2754 GLN cc_start: 0.9422 (tp-100) cc_final: 0.8766 (tm130) REVERT: D 2757 MET cc_start: 0.6298 (mpt) cc_final: 0.5764 (mpt) REVERT: D 2782 MET cc_start: 0.8150 (ptm) cc_final: 0.7619 (ptm) REVERT: D 2840 MET cc_start: 0.7777 (mmt) cc_final: 0.7332 (mmt) REVERT: D 2843 MET cc_start: 0.8643 (tpt) cc_final: 0.7773 (tpt) REVERT: D 2847 ASN cc_start: 0.9351 (t0) cc_final: 0.9005 (t0) REVERT: D 2880 LYS cc_start: 0.9276 (mppt) cc_final: 0.8855 (mppt) REVERT: D 2897 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8781 (mm-40) REVERT: D 2980 LEU cc_start: 0.8988 (tt) cc_final: 0.8667 (tm) REVERT: D 3003 MET cc_start: 0.8665 (ptm) cc_final: 0.7910 (ptp) REVERT: D 3007 LEU cc_start: 0.9099 (mt) cc_final: 0.8752 (mm) REVERT: D 3021 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6892 (mp) REVERT: D 3057 LEU cc_start: 0.9154 (tm) cc_final: 0.8815 (pp) REVERT: D 3072 MET cc_start: 0.9269 (ttt) cc_final: 0.8735 (tmm) REVERT: D 3104 MET cc_start: 0.8767 (ptt) cc_final: 0.7965 (tmm) REVERT: D 3115 HIS cc_start: 0.7969 (m90) cc_final: 0.7400 (m90) REVERT: D 3131 TYR cc_start: 0.8780 (m-10) cc_final: 0.8562 (m-80) REVERT: D 3137 LEU cc_start: 0.9420 (mm) cc_final: 0.9194 (mp) REVERT: D 3162 PHE cc_start: 0.9059 (t80) cc_final: 0.8820 (t80) REVERT: D 3246 MET cc_start: 0.7750 (mmt) cc_final: 0.7434 (mpt) REVERT: D 3252 HIS cc_start: 0.8181 (m90) cc_final: 0.7800 (m-70) REVERT: D 3263 MET cc_start: 0.8307 (mmm) cc_final: 0.7657 (mpm) REVERT: D 3295 TRP cc_start: 0.7945 (p-90) cc_final: 0.7377 (p-90) REVERT: D 3296 MET cc_start: 0.9138 (ptp) cc_final: 0.8375 (ptp) REVERT: D 3719 MET cc_start: 0.7690 (tpp) cc_final: 0.7459 (tpt) REVERT: D 4306 PHE cc_start: 0.7507 (m-80) cc_final: 0.7136 (m-10) outliers start: 98 outliers final: 45 residues processed: 989 average time/residue: 2.0700 time to fit residues: 2975.8241 Evaluate side-chains 1008 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 938 time to evaluate : 11.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3250 TRP Chi-restraints excluded: chain A residue 3269 ASN Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1060 TYR Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3117 PHE Chi-restraints excluded: chain B residue 3250 TRP Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3117 PHE Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3233 HIS Chi-restraints excluded: chain D residue 4258 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 10.0000 chunk 1641 optimal weight: 1.9990 chunk 1001 optimal weight: 10.0000 chunk 778 optimal weight: 2.9990 chunk 1140 optimal weight: 9.9990 chunk 1721 optimal weight: 3.9990 chunk 1584 optimal weight: 3.9990 chunk 1370 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 1058 optimal weight: 6.9990 chunk 840 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3116 GLN ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3179 ASN A3233 HIS A3269 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2927 GLN ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS B3269 ASN ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3116 GLN ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3233 HIS D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 141628 Z= 0.292 Angle : 0.661 21.195 191356 Z= 0.325 Chirality : 0.042 0.342 20988 Planarity : 0.005 0.125 24588 Dihedral : 5.319 78.527 19028 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 0.62 % Allowed : 9.26 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.06), residues: 17212 helix: 1.82 (0.05), residues: 9000 sheet: 0.24 (0.13), residues: 1512 loop : -0.37 (0.07), residues: 6700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B3249 HIS 0.031 0.001 HIS D3233 PHE 0.058 0.002 PHE A2943 TYR 0.052 0.001 TYR B3131 ARG 0.015 0.000 ARG B4046 ********************** 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 1034 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 946 time to evaluate : 11.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 241 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7043 (pmm) REVERT: A 878 LEU cc_start: 0.8944 (mp) cc_final: 0.8725 (pt) REVERT: A 940 LEU cc_start: 0.9320 (mt) cc_final: 0.9014 (pp) REVERT: A 946 LEU cc_start: 0.8648 (mt) cc_final: 0.8221 (pp) REVERT: A 995 MET cc_start: 0.8120 (mtm) cc_final: 0.7810 (mtt) REVERT: A 1050 LEU cc_start: 0.9332 (mm) cc_final: 0.9011 (tp) REVERT: A 2142 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7929 (tpp) REVERT: A 2688 MET cc_start: 0.6596 (mmt) cc_final: 0.5892 (mpp) REVERT: A 2689 MET cc_start: 0.5895 (tmm) cc_final: 0.5562 (mpt) REVERT: A 2695 MET cc_start: 0.3555 (mmm) cc_final: 0.3176 (mmm) REVERT: A 2723 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8248 (mtmm) REVERT: A 2724 TYR cc_start: 0.8974 (t80) cc_final: 0.8700 (t80) REVERT: A 2727 HIS cc_start: 0.9398 (t-90) cc_final: 0.9140 (m-70) REVERT: A 2757 MET cc_start: 0.6941 (mtt) cc_final: 0.6601 (mpt) REVERT: A 2772 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8201 (mtm110) REVERT: A 2782 MET cc_start: 0.8541 (ptm) cc_final: 0.8207 (ppp) REVERT: A 2840 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: A 2843 MET cc_start: 0.8211 (tpt) cc_final: 0.7423 (tpt) REVERT: A 2844 MET cc_start: 0.9017 (ppp) cc_final: 0.8734 (ppp) REVERT: A 2877 LEU cc_start: 0.8800 (mt) cc_final: 0.8481 (mt) REVERT: A 2880 LYS cc_start: 0.9319 (mppt) cc_final: 0.8989 (mppt) REVERT: A 2895 PHE cc_start: 0.8970 (t80) cc_final: 0.7831 (t80) REVERT: A 2939 TYR cc_start: 0.8607 (m-80) cc_final: 0.8298 (m-80) REVERT: A 2980 LEU cc_start: 0.9075 (tt) cc_final: 0.8786 (tm) REVERT: A 2982 PHE cc_start: 0.8089 (m-80) cc_final: 0.7669 (m-10) REVERT: A 3003 MET cc_start: 0.8781 (ptm) cc_final: 0.8428 (ptm) REVERT: A 3021 LEU cc_start: 0.7149 (tp) cc_final: 0.6866 (mp) REVERT: A 3034 HIS cc_start: 0.8304 (m90) cc_final: 0.7945 (m90) REVERT: A 3104 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: A 3117 PHE cc_start: 0.8758 (t80) cc_final: 0.7565 (t80) REVERT: A 3131 TYR cc_start: 0.9243 (m-10) cc_final: 0.8896 (m-80) REVERT: A 3241 MET cc_start: 0.9115 (mmp) cc_final: 0.8505 (mmm) REVERT: A 3246 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7461 (pmm) REVERT: A 3250 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.7127 (m100) REVERT: A 3252 HIS cc_start: 0.8329 (m90) cc_final: 0.7895 (m-70) REVERT: A 3269 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8328 (p0) REVERT: A 3272 HIS cc_start: 0.8483 (m90) cc_final: 0.7696 (m90) REVERT: A 3295 TRP cc_start: 0.8274 (p-90) cc_final: 0.7927 (p-90) REVERT: A 3296 MET cc_start: 0.9168 (ptp) cc_final: 0.8787 (ptp) REVERT: F 19 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8707 (mmmm) REVERT: F 26 HIS cc_start: 0.9291 (OUTLIER) cc_final: 0.8592 (m-70) REVERT: B 940 LEU cc_start: 0.9254 (mt) cc_final: 0.8925 (pp) REVERT: B 946 LEU cc_start: 0.8862 (mt) cc_final: 0.8469 (pp) REVERT: B 995 MET cc_start: 0.8392 (mtm) cc_final: 0.7955 (mtt) REVERT: B 1050 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9178 (tp) REVERT: B 1113 MET cc_start: 0.8823 (mtm) cc_final: 0.8599 (mtp) REVERT: B 1165 MET cc_start: 0.8370 (mpp) cc_final: 0.8036 (mtm) REVERT: B 2688 MET cc_start: 0.6268 (mpp) cc_final: 0.5837 (mmp) REVERT: B 2689 MET cc_start: 0.5395 (tmm) cc_final: 0.5037 (mpm) REVERT: B 2695 MET cc_start: 0.4326 (mmm) cc_final: 0.3825 (mmm) REVERT: B 2730 ASP cc_start: 0.9224 (m-30) cc_final: 0.8892 (t0) REVERT: B 2754 GLN cc_start: 0.9371 (tp-100) cc_final: 0.8561 (pp30) REVERT: B 2757 MET cc_start: 0.6842 (mtt) cc_final: 0.6472 (mmp) REVERT: B 2772 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7791 (tpp80) REVERT: B 2840 MET cc_start: 0.7708 (mmt) cc_final: 0.7346 (mmt) REVERT: B 2843 MET cc_start: 0.8331 (tpt) cc_final: 0.7558 (tpt) REVERT: B 2844 MET cc_start: 0.9154 (ppp) cc_final: 0.8872 (ppp) REVERT: B 2847 ASN cc_start: 0.8971 (t0) cc_final: 0.8707 (t0) REVERT: B 2884 LYS cc_start: 0.9076 (pptt) cc_final: 0.8862 (tmmt) REVERT: B 2895 PHE cc_start: 0.9106 (t80) cc_final: 0.8635 (t80) REVERT: B 2939 TYR cc_start: 0.8693 (m-80) cc_final: 0.8433 (m-80) REVERT: B 3036 LEU cc_start: 0.9293 (mp) cc_final: 0.8668 (tt) REVERT: B 3072 MET cc_start: 0.8632 (mmm) cc_final: 0.8401 (tpp) REVERT: B 3117 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 3250 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7558 (m100) REVERT: B 3252 HIS cc_start: 0.8241 (m90) cc_final: 0.7747 (m-70) REVERT: B 3273 MET cc_start: 0.9476 (mpm) cc_final: 0.9031 (mpm) REVERT: B 3295 TRP cc_start: 0.8615 (p-90) cc_final: 0.8223 (p-90) REVERT: B 3296 MET cc_start: 0.9198 (ptp) cc_final: 0.8877 (ptp) REVERT: B 3719 MET cc_start: 0.7926 (tpp) cc_final: 0.7693 (tpt) REVERT: B 3819 MET cc_start: 0.5809 (pmt) cc_final: 0.5573 (pmt) REVERT: B 4048 PHE cc_start: 0.8725 (t80) cc_final: 0.8503 (t80) REVERT: B 4258 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7901 (ptm) REVERT: B 4306 PHE cc_start: 0.7622 (m-80) cc_final: 0.7286 (m-10) REVERT: C 241 MET cc_start: 0.7683 (mpp) cc_final: 0.7480 (pmm) REVERT: C 678 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: C 940 LEU cc_start: 0.9310 (mt) cc_final: 0.8903 (pp) REVERT: C 946 LEU cc_start: 0.8569 (mt) cc_final: 0.8081 (pp) REVERT: C 964 MET cc_start: 0.1321 (OUTLIER) cc_final: 0.0728 (pmm) REVERT: C 995 MET cc_start: 0.8017 (mtm) cc_final: 0.7651 (mtt) REVERT: C 999 LEU cc_start: 0.9105 (tp) cc_final: 0.8835 (mm) REVERT: C 1050 LEU cc_start: 0.9424 (mm) cc_final: 0.9167 (tp) REVERT: C 1721 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7542 (mmp) REVERT: C 2150 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: C 2456 MET cc_start: 0.8280 (mmm) cc_final: 0.8036 (mmm) REVERT: C 2584 MET cc_start: 0.8489 (ptm) cc_final: 0.8287 (ptm) REVERT: C 2662 PHE cc_start: 0.8352 (m-10) cc_final: 0.8083 (m-10) REVERT: C 2688 MET cc_start: 0.6264 (mmt) cc_final: 0.5798 (mpp) REVERT: C 2689 MET cc_start: 0.6024 (tmm) cc_final: 0.5323 (mpt) REVERT: C 2723 LYS cc_start: 0.9397 (mtpt) cc_final: 0.8992 (mmtm) REVERT: C 2782 MET cc_start: 0.8617 (ptm) cc_final: 0.8387 (ppp) REVERT: C 2828 MET cc_start: 0.7947 (mmm) cc_final: 0.7714 (mpp) REVERT: C 2840 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6949 (mmt) REVERT: C 2843 MET cc_start: 0.8161 (tpt) cc_final: 0.7352 (tpt) REVERT: C 2844 MET cc_start: 0.9022 (ppp) cc_final: 0.8707 (ppp) REVERT: C 2877 LEU cc_start: 0.8813 (mt) cc_final: 0.8414 (mt) REVERT: C 2880 LYS cc_start: 0.9317 (mppt) cc_final: 0.9039 (mppt) REVERT: C 2895 PHE cc_start: 0.9138 (t80) cc_final: 0.8660 (t80) REVERT: C 2899 ASN cc_start: 0.8664 (m-40) cc_final: 0.8062 (m110) REVERT: C 2975 PHE cc_start: 0.8556 (m-10) cc_final: 0.8302 (m-10) REVERT: C 3021 LEU cc_start: 0.7108 (tp) cc_final: 0.6769 (mp) REVERT: C 3108 LEU cc_start: 0.9362 (mt) cc_final: 0.8674 (mt) REVERT: C 3111 HIS cc_start: 0.8273 (p-80) cc_final: 0.7621 (p90) REVERT: C 3117 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8717 (t80) REVERT: C 3246 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7759 (pmm) REVERT: C 3249 TRP cc_start: 0.8231 (m-10) cc_final: 0.7952 (m-10) REVERT: C 3250 TRP cc_start: 0.8270 (m100) cc_final: 0.7197 (m100) REVERT: C 3252 HIS cc_start: 0.8301 (m90) cc_final: 0.7788 (m90) REVERT: C 3277 LEU cc_start: 0.9393 (tp) cc_final: 0.9069 (pp) REVERT: C 3287 ASN cc_start: 0.8849 (t0) cc_final: 0.8485 (p0) REVERT: D 241 MET cc_start: 0.6825 (pmm) cc_final: 0.6600 (pmm) REVERT: D 395 HIS cc_start: 0.7926 (m-70) cc_final: 0.7619 (m-70) REVERT: D 678 MET cc_start: 0.8165 (tpp) cc_final: 0.7824 (ttp) REVERT: D 1168 MET cc_start: 0.8578 (mmm) cc_final: 0.8302 (mmp) REVERT: D 1975 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7968 (ppp) REVERT: D 2150 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7207 (mpp) REVERT: D 2192 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8109 (tpt) REVERT: D 2347 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.7766 (mpt) REVERT: D 2540 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7977 (p-80) REVERT: D 2585 MET cc_start: 0.8687 (ttp) cc_final: 0.8469 (ttp) REVERT: D 2652 LEU cc_start: 0.9074 (tp) cc_final: 0.8643 (tm) REVERT: D 2695 MET cc_start: 0.6699 (mmm) cc_final: 0.6159 (mmm) REVERT: D 2724 TYR cc_start: 0.9004 (t80) cc_final: 0.8588 (t80) REVERT: D 2754 GLN cc_start: 0.9424 (tp-100) cc_final: 0.8765 (tm130) REVERT: D 2782 MET cc_start: 0.8178 (ptm) cc_final: 0.7656 (ptm) REVERT: D 2840 MET cc_start: 0.7762 (mmt) cc_final: 0.7329 (mmt) REVERT: D 2843 MET cc_start: 0.8588 (tpt) cc_final: 0.7646 (tpt) REVERT: D 2847 ASN cc_start: 0.9345 (t0) cc_final: 0.9006 (t0) REVERT: D 2880 LYS cc_start: 0.9262 (mppt) cc_final: 0.8840 (mppt) REVERT: D 2897 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8794 (mm-40) REVERT: D 2980 LEU cc_start: 0.8998 (tt) cc_final: 0.8698 (tm) REVERT: D 3003 MET cc_start: 0.8666 (ptm) cc_final: 0.7912 (ptp) REVERT: D 3007 LEU cc_start: 0.9110 (mt) cc_final: 0.8761 (mm) REVERT: D 3021 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6926 (mp) REVERT: D 3057 LEU cc_start: 0.9156 (tm) cc_final: 0.8819 (pp) REVERT: D 3072 MET cc_start: 0.9248 (ttt) cc_final: 0.8746 (tmm) REVERT: D 3104 MET cc_start: 0.8777 (ptt) cc_final: 0.7980 (tmm) REVERT: D 3115 HIS cc_start: 0.7840 (m90) cc_final: 0.7481 (m90) REVERT: D 3131 TYR cc_start: 0.8788 (m-10) cc_final: 0.8569 (m-80) REVERT: D 3137 LEU cc_start: 0.9406 (mm) cc_final: 0.9183 (mp) REVERT: D 3162 PHE cc_start: 0.9050 (t80) cc_final: 0.8821 (t80) REVERT: D 3246 MET cc_start: 0.7755 (mmt) cc_final: 0.7393 (mpt) REVERT: D 3252 HIS cc_start: 0.8214 (m90) cc_final: 0.7804 (m-70) REVERT: D 3263 MET cc_start: 0.8290 (mmm) cc_final: 0.7633 (mpm) REVERT: D 3295 TRP cc_start: 0.7995 (p-90) cc_final: 0.7570 (p-90) REVERT: D 3296 MET cc_start: 0.9134 (ptp) cc_final: 0.8468 (ptp) REVERT: D 3719 MET cc_start: 0.7679 (tpp) cc_final: 0.7468 (tpt) REVERT: D 4306 PHE cc_start: 0.7511 (m-80) cc_final: 0.7136 (m-10) outliers start: 88 outliers final: 47 residues processed: 982 average time/residue: 1.9949 time to fit residues: 2837.1875 Evaluate side-chains 1013 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 940 time to evaluate : 10.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2347 MET Chi-restraints excluded: chain A residue 2540 HIS Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2840 MET Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3138 TYR Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3233 HIS Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3250 TRP Chi-restraints excluded: chain A residue 3269 ASN Chi-restraints excluded: chain A residue 3653 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 2540 HIS Chi-restraints excluded: chain B residue 2827 ASP Chi-restraints excluded: chain B residue 2932 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3117 PHE Chi-restraints excluded: chain B residue 3233 HIS Chi-restraints excluded: chain B residue 3250 TRP Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4258 MET Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1721 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2540 HIS Chi-restraints excluded: chain C residue 2827 ASP Chi-restraints excluded: chain C residue 2840 MET Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3117 PHE Chi-restraints excluded: chain C residue 3138 TYR Chi-restraints excluded: chain C residue 3181 TYR Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4520 TYR Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2540 HIS Chi-restraints excluded: chain D residue 2827 ASP Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3819 MET Chi-restraints excluded: chain D residue 4258 MET Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 7.9990 chunk 1460 optimal weight: 1.9990 chunk 419 optimal weight: 7.9990 chunk 1264 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 380 optimal weight: 4.9990 chunk 1373 optimal weight: 0.7980 chunk 574 optimal weight: 10.0000 chunk 1409 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2613 HIS ** A2659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3116 GLN ** A3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3233 HIS A3269 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS B3269 ASN ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3114 GLN ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3256 ASN C3272 HIS ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2977 ASN ** D3017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3269 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.051744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.037411 restraints weight = 1217191.520| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.87 r_work: 0.2978 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2515 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= 0.199 Angle : 0.644 21.085 191356 Z= 0.315 Chirality : 0.041 0.352 20988 Planarity : 0.004 0.124 24588 Dihedral : 5.241 78.196 19028 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 0.65 % Allowed : 9.31 % Favored : 90.04 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.06), residues: 17212 helix: 1.86 (0.05), residues: 8996 sheet: 0.28 (0.13), residues: 1520 loop : -0.32 (0.07), residues: 6696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C3295 HIS 0.015 0.001 HIS A3115 PHE 0.060 0.001 PHE B2943 TYR 0.048 0.001 TYR C 931 ARG 0.014 0.000 ARG B4046 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48556.34 seconds wall clock time: 841 minutes 46.06 seconds (50506.06 seconds total)