Starting phenix.real_space_refine on Thu Mar 21 03:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9t_26408/03_2024/7u9t_26408_updated.pdb" } resolution = 2.68 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= 0.015 sd= 0.035 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 976 5.16 5 C 91060 2.51 5 N 24372 2.21 5 O 26800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3642": "OE1" <-> "OE2" Residue "A PHE 3906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "I PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1196": "OD1" <-> "OD2" Residue "D PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3642": "OE1" <-> "OE2" Residue "D PHE 3906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 913": "NH1" <-> "NH2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1196": "OD1" <-> "OD2" Residue "B PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3642": "OE1" <-> "OE2" Residue "B PHE 3906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 913": "NH1" <-> "NH2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1196": "OD1" <-> "OD2" Residue "C PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3642": "OE1" <-> "OE2" Residue "C PHE 3906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143236 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 33816 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 34530 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: "I" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 33816 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 34530 Chain: "B" Number of atoms: 33816 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 34530 Chain: "C" Number of atoms: 33816 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 4229, 33808 Classifications: {'peptide': 4229} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4072} 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: 34530 Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33955 SG CYS A4888 179.250 203.586 122.905 1.00 61.65 S ATOM 33980 SG CYS A4891 178.220 201.327 120.016 1.00 60.33 S ATOM 71337 SG CYS D4888 171.197 179.280 122.916 1.00 61.68 S ATOM 71362 SG CYS D4891 173.460 178.247 120.030 1.00 61.37 S ATOM A03Z5 SG CYS B4888 203.394 195.306 122.801 1.00 60.88 S ATOM A03ZU SG CYS B4891 201.131 196.348 119.920 1.00 62.66 S ATOM A0U2H SG CYS C4888 195.266 170.908 122.757 1.00 63.72 S ATOM A0U36 SG CYS C4891 196.297 173.169 119.870 1.00 63.01 S Time building chain proxies: 98.69, per 1000 atoms: 0.69 Number of scatterers: 143236 At special positions: 0 Unit cell: (375.232, 375.232, 210.496, 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 976 16.00 P 24 15.00 O 26800 8.00 N 24372 7.00 C 91060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " 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: 43.24 Conformation dependent library (CDL) restraints added in 36.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33568 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: 712 helices and 76 sheets defined 59.1% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.73 Creating SS restraints... Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.656A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.244A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.934A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.655A 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: 3.934A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.655A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.245A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.934A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.656A 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: 3.934A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.868A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.991A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.636A pdb=" N HIS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.590A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.997A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 4.039A pdb=" N VAL A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 493 removed outlier: 3.835A pdb=" N GLY A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.752A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.724A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.160A pdb=" N SER A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.775A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.116A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.588A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.649A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 589' Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.630A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.635A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.635A 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: 4.737A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.457A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 876 through 901 removed outlier: 3.897A pdb=" N ILE A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.105A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 5.391A 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: 4.193A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.843A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.588A 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: 7.151A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 4.055A 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: 3.918A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.334A 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: 3.953A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.330A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.601A 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: 3.674A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.932A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 4.792A pdb=" N ILE A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 3.964A pdb=" N ALA A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 4.126A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.770A pdb=" N LEU A1804 " --> pdb=" O LYS A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 4.063A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1955 removed outlier: 3.684A pdb=" N VAL A1926 " --> pdb=" O ILE A1922 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1950 " --> pdb=" O GLU A1946 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1967 removed outlier: 3.788A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 removed outlier: 4.121A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 4.088A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.703A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A2073 " --> pdb=" O TRP A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.740A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2106 removed outlier: 3.677A pdb=" N ARG A2100 " --> pdb=" O GLY A2096 " (cutoff:3.500A) Proline residue: A2103 - end of helix removed outlier: 5.642A pdb=" N TYR A2106 " --> pdb=" O LEU A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.790A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A2129 " --> pdb=" O GLN A2125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 3.732A pdb=" N LEU A2141 " --> pdb=" O GLU A2137 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.090A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.512A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.641A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 removed outlier: 3.503A pdb=" N SER A2225 " --> pdb=" O LEU A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2248 removed outlier: 3.567A pdb=" N VAL A2247 " --> pdb=" O ALA A2243 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.564A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A2264 " --> pdb=" O PRO A2260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.892A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.713A pdb=" N ASN A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 3.616A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2337' Processing helix chain 'A' and resid 2342 through 2357 removed outlier: 4.179A pdb=" N ALA A2346 " --> pdb=" O GLY A2342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A2351 " --> pdb=" O MET A2347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU A2355 " --> pdb=" O ILE A2351 " (cutoff:3.500A) Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2412 removed outlier: 3.810A pdb=" N ILE A2388 " --> pdb=" O MET A2384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A2396 " --> pdb=" O TYR A2392 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A2403 " --> pdb=" O LEU A2399 " (cutoff:3.500A) Proline residue: A2404 - end of helix removed outlier: 8.942A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 removed outlier: 3.523A pdb=" N ILE A2427 " --> pdb=" O LEU A2423 " (cutoff:3.500A) Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 removed outlier: 3.802A pdb=" N VAL A2435 " --> pdb=" O ASP A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.699A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A2467 " --> pdb=" O ASP A2463 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 5.030A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 3.508A pdb=" N SER A2501 " --> pdb=" O ARG A2497 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A2502 " --> pdb=" O ALA A2498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.854A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 3.883A pdb=" N VAL A2524 " --> pdb=" O LEU A2520 " (cutoff:3.500A) removed outlier: 5.593A 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: 4.186A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A2550 " --> pdb=" O ASP A2546 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2581 removed outlier: 3.897A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A2580 " --> pdb=" O ILE A2576 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG A2581 " --> pdb=" O CYS A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2585 through 2596 removed outlier: 3.952A pdb=" N LEU A2589 " --> pdb=" O MET A2585 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 4.054A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.268A 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 2715 through 2740 removed outlier: 4.561A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.247A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2784 removed outlier: 4.823A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A2772 " --> pdb=" O LYS A2768 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 removed outlier: 3.670A pdb=" N MET A2843 " --> pdb=" O ALA A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2878 through 2900 removed outlier: 4.260A pdb=" N ALA A2883 " --> pdb=" O ALA A2879 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG A2886 " --> pdb=" O LYS A2882 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2947 removed outlier: 3.959A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 5.089A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.906A pdb=" N ARG A2979 " --> pdb=" O PHE A2975 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 3.794A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 removed outlier: 3.967A pdb=" N THR A3039 " --> pdb=" O ILE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 3.633A pdb=" N GLN A3079 " --> pdb=" O LEU A3075 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.664A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3144 removed outlier: 6.654A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3153 removed outlier: 4.253A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER A3153 " --> pdb=" O GLU A3149 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 5.143A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 3.854A pdb=" N ALA A3194 " --> pdb=" O ARG A3190 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 3.668A pdb=" N VAL A3204 " --> pdb=" O ASN A3200 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix No H-bonds generated for 'chain 'A' and resid 3200 through 3206' Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.759A 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 3237 through 3250 removed outlier: 3.509A pdb=" N MET A3241 " --> pdb=" O VAL A3237 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3258 removed outlier: 4.136A 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 3288 Processing helix chain 'A' and resid 3293 through 3307 removed outlier: 4.019A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix Processing helix chain 'A' and resid 3311 through 3316 Processing helix chain 'A' and resid 3317 through 3330 Proline residue: A3321 - end of helix Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.885A pdb=" N ALA A3598 " --> pdb=" O GLN A3594 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A3599 " --> pdb=" O ARG A3595 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A3600 " --> pdb=" O LYS A3596 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A3601 " --> pdb=" O ARG A3597 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS A3602 " --> pdb=" O ALA A3598 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A3603 " --> pdb=" O VAL A3599 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.672A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 3.601A pdb=" N GLU A3625 " --> pdb=" O LEU A3621 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A3626 " --> pdb=" O GLN A3622 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 removed outlier: 3.528A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.694A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.638A pdb=" N CYS A3699 " --> pdb=" O MET A3695 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS A3700 " --> pdb=" O ALA A3696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A3701 " --> pdb=" O LYS A3697 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.866A pdb=" N LEU A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 removed outlier: 3.646A pdb=" N THR A3758 " --> pdb=" O MET A3754 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A3760 " --> pdb=" O ALA A3756 " (cutoff:3.500A) Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.340A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.538A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 4.253A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 3.623A pdb=" N TYR A3892 " --> pdb=" O PHE A3888 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 removed outlier: 3.516A pdb=" N ASN A3905 " --> pdb=" O GLN A3901 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 3.813A pdb=" N SER A3938 " --> pdb=" O SER A3934 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 3.824A pdb=" N GLY A3946 " --> pdb=" O ASP A3942 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 removed outlier: 3.990A pdb=" N LEU A3968 " --> pdb=" O GLN A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.763A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.051A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.125A pdb=" N LYS A4085 " --> pdb=" O GLU A4081 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A4087 " --> pdb=" O PHE A4083 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A4088 " --> pdb=" O VAL A4084 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.790A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.572A pdb=" N GLU A4120 " --> pdb=" O GLN A4116 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A4121 " --> pdb=" O THR A4117 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A4122 " --> pdb=" O PHE A4118 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4181 through 4208 removed outlier: 4.791A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4262 removed outlier: 4.216A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4273 removed outlier: 4.603A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.318A pdb=" N ILE A4485 " --> pdb=" O TRP A4481 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.800A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.055A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 3.927A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4675 through 4683 Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.201A 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: 3.861A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4750 removed outlier: 4.877A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.887A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.224A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 3.504A pdb=" N GLY A4820 " --> pdb=" O HIS A4816 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.446A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A4831 " --> pdb=" O ILE A4827 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4826 through 4831' Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 removed outlier: 4.061A pdb=" N ILE A4862 " --> pdb=" O LEU A4858 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A4863 " --> pdb=" O LEU A4859 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.851A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 4.215A 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: 4.533A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A1776 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1772 through 1778' Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.862A pdb=" N ALA A 328 " --> pdb=" O ASP A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.868A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.992A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.636A pdb=" N HIS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 271' Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.590A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.997A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 removed outlier: 4.038A pdb=" N VAL D 452 " --> pdb=" O PRO D 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 493 removed outlier: 3.836A pdb=" N GLY D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.752A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.725A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.160A pdb=" N SER D 525 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE D 529 " --> pdb=" O SER D 525 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.774A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.115A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.588A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.649A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 589' Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.630A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.635A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.635A 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: 4.738A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.458A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 876 through 901 removed outlier: 3.897A pdb=" N ILE D 881 " --> pdb=" O HIS D 877 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.104A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 5.391A 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: 4.193A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.843A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.588A 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: 7.151A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.919A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.335A 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: 3.954A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.330A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.601A 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: 3.674A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.932A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 removed outlier: 4.792A pdb=" N ILE D1689 " --> pdb=" O LEU D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 3.964A pdb=" N ALA D1715 " --> pdb=" O LEU D1711 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 4.126A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.770A pdb=" N LEU D1804 " --> pdb=" O LYS D1800 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 4.063A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1955 removed outlier: 3.684A pdb=" N VAL D1926 " --> pdb=" O ILE D1922 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D1950 " --> pdb=" O GLU D1946 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1967 removed outlier: 3.787A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 removed outlier: 4.121A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 4.087A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.704A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D2073 " --> pdb=" O TRP D2069 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.740A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2106 removed outlier: 3.678A pdb=" N ARG D2100 " --> pdb=" O GLY D2096 " (cutoff:3.500A) Proline residue: D2103 - end of helix removed outlier: 5.643A pdb=" N TYR D2106 " --> pdb=" O LEU D2102 " (cutoff:3.500A) Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.790A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D2129 " --> pdb=" O GLN D2125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 3.732A pdb=" N LEU D2141 " --> pdb=" O GLU D2137 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.089A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.512A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.641A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 removed outlier: 3.503A pdb=" N SER D2225 " --> pdb=" O LEU D2221 " (cutoff:3.500A) Processing helix chain 'D' and resid 2238 through 2248 removed outlier: 3.568A pdb=" N VAL D2247 " --> pdb=" O ALA D2243 " (cutoff:3.500A) Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.564A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D2264 " --> pdb=" O PRO D2260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.891A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.713A pdb=" N ASN D2318 " --> pdb=" O GLU D2314 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 3.615A pdb=" N ARG D2336 " --> pdb=" O GLY D2332 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2332 through 2337' Processing helix chain 'D' and resid 2342 through 2357 removed outlier: 4.179A pdb=" N ALA D2346 " --> pdb=" O GLY D2342 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D2351 " --> pdb=" O MET D2347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU D2355 " --> pdb=" O ILE D2351 " (cutoff:3.500A) Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2412 removed outlier: 3.810A pdb=" N ILE D2388 " --> pdb=" O MET D2384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D2396 " --> pdb=" O TYR D2392 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D2403 " --> pdb=" O LEU D2399 " (cutoff:3.500A) Proline residue: D2404 - end of helix removed outlier: 8.940A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 removed outlier: 3.523A pdb=" N ILE D2427 " --> pdb=" O LEU D2423 " (cutoff:3.500A) Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 removed outlier: 3.803A pdb=" N VAL D2435 " --> pdb=" O ASP D2431 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.699A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA D2467 " --> pdb=" O ASP D2463 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 5.030A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 3.507A pdb=" N SER D2501 " --> pdb=" O ARG D2497 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D2502 " --> pdb=" O ALA D2498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.854A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 3.882A pdb=" N VAL D2524 " --> pdb=" O LEU D2520 " (cutoff:3.500A) removed outlier: 5.593A 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: 4.186A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS D2550 " --> pdb=" O ASP D2546 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2581 removed outlier: 3.898A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D2580 " --> pdb=" O ILE D2576 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG D2581 " --> pdb=" O CYS D2577 " (cutoff:3.500A) Processing helix chain 'D' and resid 2585 through 2596 removed outlier: 3.952A pdb=" N LEU D2589 " --> pdb=" O MET D2585 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 4.054A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.269A 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 2715 through 2740 removed outlier: 4.561A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.247A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2767 through 2784 removed outlier: 4.823A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D2772 " --> pdb=" O LYS D2768 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 removed outlier: 3.670A pdb=" N MET D2843 " --> pdb=" O ALA D2839 " (cutoff:3.500A) Processing helix chain 'D' and resid 2878 through 2900 removed outlier: 4.260A pdb=" N ALA D2883 " --> pdb=" O ALA D2879 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG D2886 " --> pdb=" O LYS D2882 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2947 removed outlier: 3.959A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 5.090A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.906A pdb=" N ARG D2979 " --> pdb=" O PHE D2975 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 3.795A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 removed outlier: 3.966A pdb=" N THR D3039 " --> pdb=" O ILE D3035 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 3.633A pdb=" N GLN D3079 " --> pdb=" O LEU D3075 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.664A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3144 removed outlier: 6.653A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS D3144 " --> pdb=" O LEU D3140 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3153 removed outlier: 4.253A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER D3153 " --> pdb=" O GLU D3149 " (cutoff:3.500A) Processing helix chain 'D' and resid 3154 through 3166 Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 5.143A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 3.854A pdb=" N ALA D3194 " --> pdb=" O ARG D3190 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 3.667A pdb=" N VAL D3204 " --> pdb=" O ASN D3200 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix No H-bonds generated for 'chain 'D' and resid 3200 through 3206' Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.760A 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 3237 through 3250 removed outlier: 3.509A pdb=" N MET D3241 " --> pdb=" O VAL D3237 " (cutoff:3.500A) Processing helix chain 'D' and resid 3253 through 3258 removed outlier: 4.136A 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 3288 Processing helix chain 'D' and resid 3293 through 3307 removed outlier: 4.019A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix Processing helix chain 'D' and resid 3311 through 3316 Processing helix chain 'D' and resid 3317 through 3330 Proline residue: D3321 - end of helix Processing helix chain 'D' and resid 3594 through 3604 removed outlier: 3.883A pdb=" N ALA D3598 " --> pdb=" O GLN D3594 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D3599 " --> pdb=" O ARG D3595 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D3600 " --> pdb=" O LYS D3596 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D3601 " --> pdb=" O ARG D3597 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D3602 " --> pdb=" O ALA D3598 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D3603 " --> pdb=" O VAL D3599 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.671A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 3.601A pdb=" N GLU D3625 " --> pdb=" O LEU D3621 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D3626 " --> pdb=" O GLN D3622 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 removed outlier: 3.528A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.693A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.638A pdb=" N CYS D3699 " --> pdb=" O MET D3695 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS D3700 " --> pdb=" O ALA D3696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D3701 " --> pdb=" O LYS D3697 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.758A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.865A pdb=" N LEU D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 removed outlier: 3.646A pdb=" N THR D3758 " --> pdb=" O MET D3754 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D3760 " --> pdb=" O ALA D3756 " (cutoff:3.500A) Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.340A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.538A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 4.253A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 3.623A pdb=" N TYR D3892 " --> pdb=" O PHE D3888 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 removed outlier: 3.517A pdb=" N ASN D3905 " --> pdb=" O GLN D3901 " (cutoff:3.500A) Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 3.814A pdb=" N SER D3938 " --> pdb=" O SER D3934 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 3.824A pdb=" N GLY D3946 " --> pdb=" O ASP D3942 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 removed outlier: 3.989A pdb=" N LEU D3968 " --> pdb=" O GLN D3964 " (cutoff:3.500A) Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.763A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.051A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.125A pdb=" N LYS D4085 " --> pdb=" O GLU D4081 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D4087 " --> pdb=" O PHE D4083 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS D4088 " --> pdb=" O VAL D4084 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.791A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.572A pdb=" N GLU D4120 " --> pdb=" O GLN D4116 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU D4121 " --> pdb=" O THR D4117 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D4122 " --> pdb=" O PHE D4118 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4181 through 4208 removed outlier: 4.791A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4262 removed outlier: 4.216A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4273 removed outlier: 4.604A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.318A pdb=" N ILE D4485 " --> pdb=" O TRP D4481 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.800A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.055A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 3.927A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4675 through 4683 Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.201A 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: 3.861A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4750 removed outlier: 4.877A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.886A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.224A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 3.504A pdb=" N GLY D4820 " --> pdb=" O HIS D4816 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.447A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D4831 " --> pdb=" O ILE D4827 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4826 through 4831' Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 removed outlier: 4.060A pdb=" N ILE D4862 " --> pdb=" O LEU D4858 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D4863 " --> pdb=" O LEU D4859 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.850A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 4.215A 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: 4.532A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D1776 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1772 through 1778' Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.862A pdb=" N ALA D 328 " --> pdb=" O ASP D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 323 through 328' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.868A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.991A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.636A pdb=" N HIS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.591A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.996A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 4.039A pdb=" N VAL B 452 " --> pdb=" O PRO B 448 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 removed outlier: 3.835A pdb=" N GLY B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.752A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.725A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.160A pdb=" N SER B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.774A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.116A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.588A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.649A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 589' Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.629A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.635A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.634A 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: 4.737A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.457A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 876 through 901 removed outlier: 3.897A pdb=" N ILE B 881 " --> pdb=" O HIS B 877 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.104A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 5.391A 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: 4.193A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.843A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.588A 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: 7.151A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 4.053A 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: 3.919A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.335A 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: 3.954A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.330A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.601A 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: 3.674A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.933A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 removed outlier: 4.792A pdb=" N ILE B1689 " --> pdb=" O LEU B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 3.963A pdb=" N ALA B1715 " --> pdb=" O LEU B1711 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 4.127A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.770A pdb=" N LEU B1804 " --> pdb=" O LYS B1800 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 4.062A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1955 removed outlier: 3.685A pdb=" N VAL B1926 " --> pdb=" O ILE B1922 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B1950 " --> pdb=" O GLU B1946 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1967 removed outlier: 3.788A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 removed outlier: 4.121A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 4.087A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.704A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B2073 " --> pdb=" O TRP B2069 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.740A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2106 removed outlier: 3.677A pdb=" N ARG B2100 " --> pdb=" O GLY B2096 " (cutoff:3.500A) Proline residue: B2103 - end of helix removed outlier: 5.643A pdb=" N TYR B2106 " --> pdb=" O LEU B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.790A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B2129 " --> pdb=" O GLN B2125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 3.731A pdb=" N LEU B2141 " --> pdb=" O GLU B2137 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.089A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.512A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.641A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 removed outlier: 3.504A pdb=" N SER B2225 " --> pdb=" O LEU B2221 " (cutoff:3.500A) Processing helix chain 'B' and resid 2238 through 2248 removed outlier: 3.568A pdb=" N VAL B2247 " --> pdb=" O ALA B2243 " (cutoff:3.500A) Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.563A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B2264 " --> pdb=" O PRO B2260 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.892A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.714A pdb=" N ASN B2318 " --> pdb=" O GLU B2314 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 3.616A pdb=" N ARG B2336 " --> pdb=" O GLY B2332 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2337' Processing helix chain 'B' and resid 2342 through 2357 removed outlier: 4.179A pdb=" N ALA B2346 " --> pdb=" O GLY B2342 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B2351 " --> pdb=" O MET B2347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B2355 " --> pdb=" O ILE B2351 " (cutoff:3.500A) Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2412 removed outlier: 3.809A pdb=" N ILE B2388 " --> pdb=" O MET B2384 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B2396 " --> pdb=" O TYR B2392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B2403 " --> pdb=" O LEU B2399 " (cutoff:3.500A) Proline residue: B2404 - end of helix removed outlier: 8.941A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 removed outlier: 3.524A pdb=" N ILE B2427 " --> pdb=" O LEU B2423 " (cutoff:3.500A) Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 removed outlier: 3.802A pdb=" N VAL B2435 " --> pdb=" O ASP B2431 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.698A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA B2467 " --> pdb=" O ASP B2463 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 5.031A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 3.508A pdb=" N SER B2501 " --> pdb=" O ARG B2497 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B2502 " --> pdb=" O ALA B2498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.854A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 3.882A pdb=" N VAL B2524 " --> pdb=" O LEU B2520 " (cutoff:3.500A) removed outlier: 5.593A 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: 4.185A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS B2550 " --> pdb=" O ASP B2546 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2581 removed outlier: 3.896A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B2580 " --> pdb=" O ILE B2576 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG B2581 " --> pdb=" O CYS B2577 " (cutoff:3.500A) Processing helix chain 'B' and resid 2585 through 2596 removed outlier: 3.953A pdb=" N LEU B2589 " --> pdb=" O MET B2585 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 4.053A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.268A 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 2715 through 2740 removed outlier: 4.560A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.247A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2784 removed outlier: 4.823A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B2772 " --> pdb=" O LYS B2768 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 removed outlier: 3.669A pdb=" N MET B2843 " --> pdb=" O ALA B2839 " (cutoff:3.500A) Processing helix chain 'B' and resid 2878 through 2900 removed outlier: 4.260A pdb=" N ALA B2883 " --> pdb=" O ALA B2879 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG B2886 " --> pdb=" O LYS B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2947 removed outlier: 3.958A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 5.088A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.906A pdb=" N ARG B2979 " --> pdb=" O PHE B2975 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 3.794A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 removed outlier: 3.966A pdb=" N THR B3039 " --> pdb=" O ILE B3035 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 3.632A pdb=" N GLN B3079 " --> pdb=" O LEU B3075 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.665A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3144 removed outlier: 6.654A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B3144 " --> pdb=" O LEU B3140 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3153 removed outlier: 4.253A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER B3153 " --> pdb=" O GLU B3149 " (cutoff:3.500A) Processing helix chain 'B' and resid 3154 through 3166 Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 5.144A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 3.854A pdb=" N ALA B3194 " --> pdb=" O ARG B3190 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 3.667A pdb=" N VAL B3204 " --> pdb=" O ASN B3200 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix No H-bonds generated for 'chain 'B' and resid 3200 through 3206' Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.759A 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 3237 through 3250 removed outlier: 3.509A pdb=" N MET B3241 " --> pdb=" O VAL B3237 " (cutoff:3.500A) Processing helix chain 'B' and resid 3253 through 3258 removed outlier: 4.136A 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 3288 Processing helix chain 'B' and resid 3293 through 3307 removed outlier: 4.019A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix Processing helix chain 'B' and resid 3311 through 3316 Processing helix chain 'B' and resid 3317 through 3330 Proline residue: B3321 - end of helix Processing helix chain 'B' and resid 3594 through 3604 removed outlier: 3.884A pdb=" N ALA B3598 " --> pdb=" O GLN B3594 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B3599 " --> pdb=" O ARG B3595 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B3600 " --> pdb=" O LYS B3596 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B3601 " --> pdb=" O ARG B3597 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS B3602 " --> pdb=" O ALA B3598 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B3603 " --> pdb=" O VAL B3599 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.671A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 3.601A pdb=" N GLU B3625 " --> pdb=" O LEU B3621 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B3626 " --> pdb=" O GLN B3622 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 removed outlier: 3.528A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.695A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.639A pdb=" N CYS B3699 " --> pdb=" O MET B3695 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS B3700 " --> pdb=" O ALA B3696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B3701 " --> pdb=" O LYS B3697 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.865A pdb=" N LEU B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 removed outlier: 3.646A pdb=" N THR B3758 " --> pdb=" O MET B3754 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B3760 " --> pdb=" O ALA B3756 " (cutoff:3.500A) Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.341A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.539A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 4.253A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 3.623A pdb=" N TYR B3892 " --> pdb=" O PHE B3888 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 removed outlier: 3.517A pdb=" N ASN B3905 " --> pdb=" O GLN B3901 " (cutoff:3.500A) Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 3.813A pdb=" N SER B3938 " --> pdb=" O SER B3934 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 3.824A pdb=" N GLY B3946 " --> pdb=" O ASP B3942 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 removed outlier: 3.989A pdb=" N LEU B3968 " --> pdb=" O GLN B3964 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.764A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.050A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.125A pdb=" N LYS B4085 " --> pdb=" O GLU B4081 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE B4087 " --> pdb=" O PHE B4083 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS B4088 " --> pdb=" O VAL B4084 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.790A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.571A pdb=" N GLU B4120 " --> pdb=" O GLN B4116 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B4121 " --> pdb=" O THR B4117 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B4122 " --> pdb=" O PHE B4118 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4181 through 4208 removed outlier: 4.790A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4262 removed outlier: 4.216A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4273 removed outlier: 4.604A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.318A pdb=" N ILE B4485 " --> pdb=" O TRP B4481 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.799A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.055A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 3.927A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4675 through 4683 Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.201A 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: 3.861A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4750 removed outlier: 4.877A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.886A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.224A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 3.505A pdb=" N GLY B4820 " --> pdb=" O HIS B4816 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.446A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B4831 " --> pdb=" O ILE B4827 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4826 through 4831' Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 removed outlier: 4.060A pdb=" N ILE B4862 " --> pdb=" O LEU B4858 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B4863 " --> pdb=" O LEU B4859 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.850A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 4.214A 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: 4.533A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B1776 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1772 through 1778' Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.862A pdb=" N ALA B 328 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 328' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.868A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.992A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.638A pdb=" N HIS C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.591A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.997A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 removed outlier: 4.039A pdb=" N VAL C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 493 removed outlier: 3.835A pdb=" N GLY C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.751A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.724A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.159A pdb=" N SER C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 529 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.774A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.115A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.588A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.649A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 589' Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.629A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.635A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.634A 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: 4.737A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.457A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 876 through 901 removed outlier: 3.897A pdb=" N ILE C 881 " --> pdb=" O HIS C 877 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.105A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 5.391A 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: 4.193A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.844A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.588A 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: 7.151A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.919A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.335A 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: 3.953A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.330A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.601A 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: 3.673A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.933A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 removed outlier: 4.793A pdb=" N ILE C1689 " --> pdb=" O LEU C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 3.964A pdb=" N ALA C1715 " --> pdb=" O LEU C1711 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 4.126A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.770A pdb=" N LEU C1804 " --> pdb=" O LYS C1800 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 4.063A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1955 removed outlier: 3.684A pdb=" N VAL C1926 " --> pdb=" O ILE C1922 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1950 " --> pdb=" O GLU C1946 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1967 removed outlier: 3.787A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 removed outlier: 4.120A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 4.088A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.703A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C2073 " --> pdb=" O TRP C2069 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.739A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2106 removed outlier: 3.678A pdb=" N ARG C2100 " --> pdb=" O GLY C2096 " (cutoff:3.500A) Proline residue: C2103 - end of helix removed outlier: 5.643A pdb=" N TYR C2106 " --> pdb=" O LEU C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.790A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C2129 " --> pdb=" O GLN C2125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 3.732A pdb=" N LEU C2141 " --> pdb=" O GLU C2137 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.089A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.511A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.641A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 removed outlier: 3.504A pdb=" N SER C2225 " --> pdb=" O LEU C2221 " (cutoff:3.500A) Processing helix chain 'C' and resid 2238 through 2248 removed outlier: 3.569A pdb=" N VAL C2247 " --> pdb=" O ALA C2243 " (cutoff:3.500A) Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.565A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C2264 " --> pdb=" O PRO C2260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.892A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.713A pdb=" N ASN C2318 " --> pdb=" O GLU C2314 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 3.616A pdb=" N ARG C2336 " --> pdb=" O GLY C2332 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2337' Processing helix chain 'C' and resid 2342 through 2357 removed outlier: 4.180A pdb=" N ALA C2346 " --> pdb=" O GLY C2342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C2351 " --> pdb=" O MET C2347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU C2355 " --> pdb=" O ILE C2351 " (cutoff:3.500A) Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2412 removed outlier: 3.810A pdb=" N ILE C2388 " --> pdb=" O MET C2384 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE C2396 " --> pdb=" O TYR C2392 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C2403 " --> pdb=" O LEU C2399 " (cutoff:3.500A) Proline residue: C2404 - end of helix removed outlier: 8.941A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 removed outlier: 3.523A pdb=" N ILE C2427 " --> pdb=" O LEU C2423 " (cutoff:3.500A) Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 removed outlier: 3.802A pdb=" N VAL C2435 " --> pdb=" O ASP C2431 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.699A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA C2467 " --> pdb=" O ASP C2463 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 5.031A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 3.508A pdb=" N SER C2501 " --> pdb=" O ARG C2497 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C2502 " --> pdb=" O ALA C2498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.853A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 3.882A pdb=" N VAL C2524 " --> pdb=" O LEU C2520 " (cutoff:3.500A) removed outlier: 5.592A 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: 4.186A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS C2550 " --> pdb=" O ASP C2546 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2581 removed outlier: 3.896A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C2580 " --> pdb=" O ILE C2576 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG C2581 " --> pdb=" O CYS C2577 " (cutoff:3.500A) Processing helix chain 'C' and resid 2585 through 2596 removed outlier: 3.952A pdb=" N LEU C2589 " --> pdb=" O MET C2585 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 4.054A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.268A 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 2715 through 2740 removed outlier: 4.561A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.248A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2767 through 2784 removed outlier: 4.823A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C2772 " --> pdb=" O LYS C2768 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 removed outlier: 3.671A pdb=" N MET C2843 " --> pdb=" O ALA C2839 " (cutoff:3.500A) Processing helix chain 'C' and resid 2878 through 2900 removed outlier: 4.260A pdb=" N ALA C2883 " --> pdb=" O ALA C2879 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG C2886 " --> pdb=" O LYS C2882 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2947 removed outlier: 3.958A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 5.089A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.906A pdb=" N ARG C2979 " --> pdb=" O PHE C2975 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 3.795A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 removed outlier: 3.967A pdb=" N THR C3039 " --> pdb=" O ILE C3035 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 3.633A pdb=" N GLN C3079 " --> pdb=" O LEU C3075 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.664A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3144 removed outlier: 6.654A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3153 removed outlier: 4.252A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER C3153 " --> pdb=" O GLU C3149 " (cutoff:3.500A) Processing helix chain 'C' and resid 3154 through 3166 Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 5.144A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 3.854A pdb=" N ALA C3194 " --> pdb=" O ARG C3190 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 3.667A pdb=" N VAL C3204 " --> pdb=" O ASN C3200 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix No H-bonds generated for 'chain 'C' and resid 3200 through 3206' Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.759A 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 3237 through 3250 removed outlier: 3.508A pdb=" N MET C3241 " --> pdb=" O VAL C3237 " (cutoff:3.500A) Processing helix chain 'C' and resid 3253 through 3258 removed outlier: 4.136A 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 3288 Processing helix chain 'C' and resid 3293 through 3307 removed outlier: 4.018A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix Processing helix chain 'C' and resid 3311 through 3316 Processing helix chain 'C' and resid 3317 through 3330 Proline residue: C3321 - end of helix Processing helix chain 'C' and resid 3594 through 3604 removed outlier: 3.885A pdb=" N ALA C3598 " --> pdb=" O GLN C3594 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C3599 " --> pdb=" O ARG C3595 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C3600 " --> pdb=" O LYS C3596 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C3601 " --> pdb=" O ARG C3597 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS C3602 " --> pdb=" O ALA C3598 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C3603 " --> pdb=" O VAL C3599 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.671A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 3.602A pdb=" N GLU C3625 " --> pdb=" O LEU C3621 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C3626 " --> pdb=" O GLN C3622 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 removed outlier: 3.528A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.694A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.639A pdb=" N CYS C3699 " --> pdb=" O MET C3695 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS C3700 " --> pdb=" O ALA C3696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C3701 " --> pdb=" O LYS C3697 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.865A pdb=" N LEU C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 removed outlier: 3.646A pdb=" N THR C3758 " --> pdb=" O MET C3754 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C3760 " --> pdb=" O ALA C3756 " (cutoff:3.500A) Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.340A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.538A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 4.253A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 3.623A pdb=" N TYR C3892 " --> pdb=" O PHE C3888 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 removed outlier: 3.515A pdb=" N ASN C3905 " --> pdb=" O GLN C3901 " (cutoff:3.500A) Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 3.813A pdb=" N SER C3938 " --> pdb=" O SER C3934 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 3.823A pdb=" N GLY C3946 " --> pdb=" O ASP C3942 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 removed outlier: 3.989A pdb=" N LEU C3968 " --> pdb=" O GLN C3964 " (cutoff:3.500A) Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.764A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.050A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.125A pdb=" N LYS C4085 " --> pdb=" O GLU C4081 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C4087 " --> pdb=" O PHE C4083 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS C4088 " --> pdb=" O VAL C4084 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.790A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.572A pdb=" N GLU C4120 " --> pdb=" O GLN C4116 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C4121 " --> pdb=" O THR C4117 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA C4122 " --> pdb=" O PHE C4118 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4181 through 4208 removed outlier: 4.790A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4262 removed outlier: 4.216A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4273 removed outlier: 4.604A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.722A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.319A pdb=" N ILE C4485 " --> pdb=" O TRP C4481 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.800A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.054A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 3.926A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4675 through 4683 Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.201A 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: 3.860A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4750 removed outlier: 4.877A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.887A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.224A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 3.505A pdb=" N GLY C4820 " --> pdb=" O HIS C4816 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.447A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C4831 " --> pdb=" O ILE C4827 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4826 through 4831' Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 removed outlier: 4.060A pdb=" N ILE C4862 " --> pdb=" O LEU C4858 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C4863 " --> pdb=" O LEU C4859 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.851A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 4.214A 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: 4.533A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR C1776 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1772 through 1778' Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.861A pdb=" N ALA C 328 " --> pdb=" O ASP C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 328' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'I' and resid 1 through 6 removed outlier: 4.814A pdb=" N LEU I 5 " --> pdb=" O MET I 1 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1 through 6' Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.910A pdb=" N ALA I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU I 12 " --> pdb=" O GLU I 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE I 13 " --> pdb=" O GLN I 9 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 41 removed outlier: 3.620A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG I 38 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 removed outlier: 3.851A pdb=" N GLN I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 56 " --> pdb=" O MET I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 78 removed outlier: 4.184A pdb=" N ARG I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 92 removed outlier: 4.810A pdb=" N GLU I 84 " --> pdb=" O THR I 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG I 87 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE I 90 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 111 removed outlier: 3.786A pdb=" N LEU I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N HIS I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR I 111 " --> pdb=" O ARG I 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 102 through 111' Processing helix chain 'I' and resid 119 through 129 removed outlier: 4.007A pdb=" N ASP I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 126 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA I 129 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 145 removed outlier: 4.201A pdb=" N VAL I 143 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 144 " --> pdb=" O GLU I 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 6 removed outlier: 4.813A pdb=" N LEU J 5 " --> pdb=" O MET J 1 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1 through 6' Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.911A pdb=" N ALA J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU J 12 " --> pdb=" O GLU J 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE J 13 " --> pdb=" O GLN J 9 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.620A pdb=" N THR J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG J 38 " --> pdb=" O GLY J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 removed outlier: 3.851A pdb=" N GLN J 50 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 56 " --> pdb=" O MET J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 78 removed outlier: 4.186A pdb=" N ARG J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS J 76 " --> pdb=" O MET J 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 92 removed outlier: 4.812A pdb=" N GLU J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 85 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE J 90 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 111 removed outlier: 3.786A pdb=" N LEU J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG J 107 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL J 109 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 102 through 111' Processing helix chain 'J' and resid 119 through 129 removed outlier: 4.006A pdb=" N ASP J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET J 125 " --> pdb=" O GLU J 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 126 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA J 129 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 145 removed outlier: 4.201A pdb=" N VAL J 143 " --> pdb=" O TYR J 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 6 removed outlier: 4.813A pdb=" N LEU K 5 " --> pdb=" O MET K 1 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1 through 6' Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.910A pdb=" N ALA K 11 " --> pdb=" O GLU K 7 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU K 12 " --> pdb=" O GLU K 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE K 13 " --> pdb=" O GLN K 9 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 41 removed outlier: 3.620A pdb=" N THR K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.852A pdb=" N GLN K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU K 55 " --> pdb=" O ASP K 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL K 56 " --> pdb=" O MET K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 removed outlier: 4.184A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS K 76 " --> pdb=" O MET K 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 92 removed outlier: 4.810A pdb=" N GLU K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE K 90 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 111 removed outlier: 3.785A pdb=" N LEU K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR K 111 " --> pdb=" O ARG K 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 102 through 111' Processing helix chain 'K' and resid 119 through 129 removed outlier: 4.006A pdb=" N ASP K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET K 125 " --> pdb=" O GLU K 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE K 126 " --> pdb=" O VAL K 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 145 removed outlier: 4.201A pdb=" N VAL K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN K 144 " --> pdb=" O GLU K 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET K 145 " --> pdb=" O GLU K 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 6 removed outlier: 4.812A pdb=" N LEU L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1 through 6' Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.910A pdb=" N ALA L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 13 " --> pdb=" O GLN L 9 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 41 removed outlier: 3.620A pdb=" N THR L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 removed outlier: 3.852A pdb=" N GLN L 50 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 78 removed outlier: 4.185A pdb=" N ARG L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 92 removed outlier: 4.811A pdb=" N GLU L 84 " --> pdb=" O THR L 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 111 removed outlier: 3.786A pdb=" N LEU L 106 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG L 107 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 102 through 111' Processing helix chain 'L' and resid 119 through 129 removed outlier: 4.006A pdb=" N ASP L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE L 126 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA L 129 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 145 removed outlier: 4.201A pdb=" N VAL L 143 " --> pdb=" O TYR L 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'H' and resid 3 through 8 removed outlier: 4.259A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 3 through 8 removed outlier: 4.258A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'F' and resid 3 through 8 removed outlier: 4.258A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'G' and resid 3 through 8 removed outlier: 4.258A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.030A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.425A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 160 through 163 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'A' and resid 192 through 196 Processing sheet with id= 8, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.732A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 10, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 11, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 12, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.747A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.731A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 776 through 780 removed outlier: 5.415A pdb=" N GLN A 776 " --> pdb=" O GLY A1470 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A1470 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.447A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 3.822A pdb=" N GLY A1019 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 7.162A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.859A pdb=" N LEU A1283 " --> pdb=" O PHE A1555 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A1431 " --> pdb=" O GLN A1554 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1430 " --> pdb=" O ILE A1507 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.990A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 4.793A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 2741 through 2744 removed outlier: 7.306A pdb=" N ILE A2746 " --> pdb=" O PRO A2755 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.698A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.030A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.426A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 160 through 163 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'D' and resid 192 through 196 Processing sheet with id= 26, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.734A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 28, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 29, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 30, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.747A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.730A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 776 through 780 removed outlier: 5.415A pdb=" N GLN D 776 " --> pdb=" O GLY D1470 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D1470 " --> pdb=" O GLN D 776 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.447A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 3.822A pdb=" N GLY D1019 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 1147 through 1151 removed outlier: 7.162A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.860A pdb=" N LEU D1283 " --> pdb=" O PHE D1555 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D1431 " --> pdb=" O GLN D1554 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.989A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 4.792A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 2741 through 2744 removed outlier: 7.306A pdb=" N ILE D2746 " --> pdb=" O PRO D2755 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.697A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.031A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.426A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 160 through 163 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'B' and resid 192 through 196 Processing sheet with id= 44, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.733A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 46, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 47, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 48, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.746A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.731A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.416A pdb=" N GLN B 776 " --> pdb=" O GLY B1470 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B1470 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.446A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 3.823A pdb=" N GLY B1019 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 1147 through 1151 removed outlier: 7.163A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.859A pdb=" N LEU B1283 " --> pdb=" O PHE B1555 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B1431 " --> pdb=" O GLN B1554 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B1430 " --> pdb=" O ILE B1507 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.990A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 4.792A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'B' and resid 2741 through 2744 removed outlier: 7.307A pdb=" N ILE B2746 " --> pdb=" O PRO B2755 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.697A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.031A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.426A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 160 through 163 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'C' and resid 192 through 196 Processing sheet with id= 62, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.734A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 64, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 65, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 66, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.747A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.731A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.415A pdb=" N GLN C 776 " --> pdb=" O GLY C1470 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C1470 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.446A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 3.823A pdb=" N GLY C1019 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'C' and resid 1147 through 1151 removed outlier: 7.162A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.860A pdb=" N LEU C1283 " --> pdb=" O PHE C1555 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C1431 " --> pdb=" O GLN C1554 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C1430 " --> pdb=" O ILE C1507 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.989A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 4.792A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'C' and resid 2741 through 2744 removed outlier: 7.306A pdb=" N ILE C2746 " --> pdb=" O PRO C2755 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.697A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) 7085 hydrogen bonds defined for protein. 21175 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: 105.99 Time building geometry restraints manager: 47.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 46920 1.34 - 1.46: 33333 1.46 - 1.59: 64407 1.59 - 1.71: 44 1.71 - 1.83: 1592 Bond restraints: 146296 Sorted by residual: bond pdb=" CG GLN C2938 " pdb=" CD GLN C2938 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.58e+00 bond pdb=" CG GLN D2938 " pdb=" CD GLN D2938 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.31e+00 bond pdb=" CG GLN A2938 " pdb=" CD GLN A2938 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.31e+00 bond pdb=" CG GLN B2938 " pdb=" CD GLN B2938 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.31e+00 bond pdb=" CA GLN C2938 " pdb=" CB GLN C2938 " ideal model delta sigma weight residual 1.528 1.575 -0.047 1.59e-02 3.96e+03 8.74e+00 ... (remaining 146291 not shown) Histogram of bond angle deviations from ideal: 94.40 - 103.53: 1784 103.53 - 112.67: 76384 112.67 - 121.80: 88834 121.80 - 130.93: 29846 130.93 - 140.06: 756 Bond angle restraints: 197604 Sorted by residual: angle pdb=" CA GLN D2659 " pdb=" CB GLN D2659 " pdb=" CG GLN D2659 " ideal model delta sigma weight residual 114.10 133.23 -19.13 2.00e+00 2.50e-01 9.15e+01 angle pdb=" CA GLN B2659 " pdb=" CB GLN B2659 " pdb=" CG GLN B2659 " ideal model delta sigma weight residual 114.10 133.21 -19.11 2.00e+00 2.50e-01 9.13e+01 angle pdb=" CA GLN A2659 " pdb=" CB GLN A2659 " pdb=" CG GLN A2659 " ideal model delta sigma weight residual 114.10 133.19 -19.09 2.00e+00 2.50e-01 9.11e+01 angle pdb=" CA GLN C2659 " pdb=" CB GLN C2659 " pdb=" CG GLN C2659 " ideal model delta sigma weight residual 114.10 133.18 -19.08 2.00e+00 2.50e-01 9.10e+01 angle pdb=" CA GLN A2938 " pdb=" CB GLN A2938 " pdb=" CG GLN A2938 " ideal model delta sigma weight residual 114.10 132.81 -18.71 2.00e+00 2.50e-01 8.75e+01 ... (remaining 197599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 79029 17.94 - 35.88: 7248 35.88 - 53.82: 1443 53.82 - 71.76: 452 71.76 - 89.70: 128 Dihedral angle restraints: 88300 sinusoidal: 36252 harmonic: 52048 Sorted by residual: dihedral pdb=" CA HIS C2995 " pdb=" C HIS C2995 " pdb=" N ALA C2996 " pdb=" CA ALA C2996 " ideal model delta harmonic sigma weight residual 180.00 123.63 56.37 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA HIS B2995 " pdb=" C HIS B2995 " pdb=" N ALA B2996 " pdb=" CA ALA B2996 " ideal model delta harmonic sigma weight residual 180.00 123.68 56.32 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA HIS D2995 " pdb=" C HIS D2995 " pdb=" N ALA D2996 " pdb=" CA ALA D2996 " ideal model delta harmonic sigma weight residual 180.00 123.69 56.31 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 88297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 18234 0.057 - 0.113: 3143 0.113 - 0.170: 257 0.170 - 0.227: 39 0.227 - 0.284: 11 Chirality restraints: 21684 Sorted by residual: chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE D 11 " pdb=" CA ILE D 11 " pdb=" CG1 ILE D 11 " pdb=" CG2 ILE D 11 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 11 " pdb=" CA ILE B 11 " pdb=" CG1 ILE B 11 " pdb=" CG2 ILE B 11 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 21681 not shown) Planarity restraints: 25424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 520 " 0.706 9.50e-02 1.11e+02 3.16e-01 6.12e+01 pdb=" NE ARG A 520 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 520 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 520 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 520 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 520 " -0.706 9.50e-02 1.11e+02 3.16e-01 6.11e+01 pdb=" NE ARG D 520 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 520 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 520 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 520 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 520 " -0.705 9.50e-02 1.11e+02 3.16e-01 6.10e+01 pdb=" NE ARG C 520 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 520 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 520 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 520 " -0.019 2.00e-02 2.50e+03 ... (remaining 25421 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1854 2.66 - 3.22: 136078 3.22 - 3.78: 228925 3.78 - 4.34: 315804 4.34 - 4.90: 507864 Nonbonded interactions: 1190525 Sorted by model distance: nonbonded pdb=" O ARG K 75 " pdb=" NZ LYS K 78 " model vdw 2.097 2.520 nonbonded pdb=" O ARG L 75 " pdb=" NZ LYS L 78 " model vdw 2.097 2.520 nonbonded pdb=" O ARG I 75 " pdb=" NZ LYS I 78 " model vdw 2.097 2.520 nonbonded pdb=" O ARG J 75 " pdb=" NZ LYS J 78 " model vdw 2.097 2.520 nonbonded pdb=" OG SER D1662 " pdb=" OD2 ASP D1708 " model vdw 2.135 2.440 ... (remaining 1190520 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' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 6.290 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: 0.150 Extract box with map and model: 31.140 Check model and map are aligned: 1.530 Set scattering table: 0.980 Process input model: 468.500 Find NCS groups from input model: 8.090 Set up NCS constraints: 1.230 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 530.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.004 0.085 146296 Z= 0.230 Angle : 0.810 26.228 197604 Z= 0.422 Chirality : 0.043 0.284 21684 Planarity : 0.007 0.316 25424 Dihedral : 14.980 89.705 54720 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 1.89 % Allowed : 0.90 % Favored : 97.21 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.06), residues: 17776 helix: 0.80 (0.06), residues: 8964 sheet: -0.19 (0.13), residues: 1736 loop : -0.68 (0.07), residues: 7076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B2627 HIS 0.014 0.001 HIS A4055 PHE 0.056 0.002 PHE C4640 TYR 0.038 0.002 TYR D 706 ARG 0.020 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1204 time to evaluate : 12.270 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 309 MET cc_start: 0.6795 (mmp) cc_final: 0.6428 (mpm) REVERT: A 932 ASN cc_start: 0.6844 (m110) cc_final: 0.6186 (m-40) REVERT: A 1494 MET cc_start: 0.8327 (ppp) cc_final: 0.8036 (ppp) REVERT: A 1501 ASN cc_start: 0.6633 (m-40) cc_final: 0.6373 (m-40) REVERT: A 1975 MET cc_start: 0.7660 (ptt) cc_final: 0.7428 (ptp) REVERT: A 2066 MET cc_start: 0.8697 (mmp) cc_final: 0.8058 (mmp) REVERT: A 2214 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8862 (tpt) REVERT: A 2585 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (pp-130) REVERT: A 2695 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6505 (tpt) REVERT: A 2702 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6512 (OUTLIER) REVERT: A 2719 TYR cc_start: 0.8382 (t80) cc_final: 0.8041 (t80) REVERT: A 2724 TYR cc_start: 0.8978 (t80) cc_final: 0.7827 (t80) REVERT: A 2850 ASN cc_start: 0.9336 (t0) cc_final: 0.8829 (t0) REVERT: A 2867 ASN cc_start: 0.0789 (OUTLIER) cc_final: 0.0573 (p0) REVERT: A 2895 PHE cc_start: 0.8984 (t80) cc_final: 0.8583 (t80) REVERT: A 2923 TYR cc_start: 0.7939 (t80) cc_final: 0.7512 (t80) REVERT: A 3046 MET cc_start: 0.7644 (mmt) cc_final: 0.7298 (mpp) REVERT: A 3068 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7610 (tt) REVERT: A 3117 PHE cc_start: 0.8511 (m-10) cc_final: 0.8277 (m-80) REVERT: A 3123 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7271 (pt) REVERT: A 3220 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8129 (tp30) REVERT: A 3235 MET cc_start: 0.6484 (mtt) cc_final: 0.6019 (mtp) REVERT: A 3242 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 3243 CYS cc_start: 0.8126 (m) cc_final: 0.7361 (m) REVERT: A 3268 LEU cc_start: 0.6818 (mp) cc_final: 0.6559 (mt) REVERT: A 3295 TRP cc_start: 0.8540 (p-90) cc_final: 0.8107 (p-90) REVERT: A 3298 ARG cc_start: 0.8315 (ptt90) cc_final: 0.8019 (mtm110) REVERT: A 3299 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 3323 MET cc_start: 0.7431 (mmp) cc_final: 0.7192 (mmm) REVERT: A 3605 MET cc_start: 0.2844 (OUTLIER) cc_final: 0.1314 (tpp) REVERT: A 4292 MET cc_start: 0.8108 (mmm) cc_final: 0.7848 (mmm) REVERT: I 64 ILE cc_start: 0.8260 (mm) cc_final: 0.7976 (tt) REVERT: I 146 MET cc_start: 0.0360 (ptt) cc_final: 0.0107 (pmm) REVERT: D 241 MET cc_start: 0.5615 (mmp) cc_final: 0.5242 (mmt) REVERT: D 317 MET cc_start: 0.7547 (ptt) cc_final: 0.7286 (ptt) REVERT: D 893 TRP cc_start: 0.7794 (m-90) cc_final: 0.7565 (m100) REVERT: D 1064 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7609 (mp) REVERT: D 1948 MET cc_start: 0.7115 (mmt) cc_final: 0.6880 (tpt) REVERT: D 2702 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 2719 TYR cc_start: 0.8502 (t80) cc_final: 0.8170 (t80) REVERT: D 2724 TYR cc_start: 0.8956 (t80) cc_final: 0.8740 (t80) REVERT: D 2779 LEU cc_start: 0.9144 (mt) cc_final: 0.8662 (mt) REVERT: D 2782 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7899 (ppp) REVERT: D 2785 TRP cc_start: 0.8015 (m-10) cc_final: 0.7811 (m-10) REVERT: D 2798 MET cc_start: 0.8927 (mmt) cc_final: 0.8506 (mmt) REVERT: D 2870 LEU cc_start: 0.8626 (mt) cc_final: 0.8301 (mm) REVERT: D 2895 PHE cc_start: 0.9152 (t80) cc_final: 0.8835 (t80) REVERT: D 3043 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7627 (mmp80) REVERT: D 3068 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8398 (tt) REVERT: D 3131 TYR cc_start: 0.8394 (m-10) cc_final: 0.8182 (m-80) REVERT: D 3211 LEU cc_start: 0.8846 (tp) cc_final: 0.8503 (pt) REVERT: D 3233 HIS cc_start: 0.7890 (t-90) cc_final: 0.7678 (t-90) REVERT: D 3235 MET cc_start: 0.6646 (mtt) cc_final: 0.6312 (mtp) REVERT: D 3242 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8478 (pp) REVERT: D 3246 MET cc_start: 0.8457 (ttp) cc_final: 0.8089 (ttp) REVERT: D 3323 MET cc_start: 0.6868 (mmp) cc_final: 0.6604 (mpm) REVERT: D 3605 MET cc_start: 0.3108 (OUTLIER) cc_final: 0.1507 (mmm) REVERT: B 309 MET cc_start: 0.7173 (mmp) cc_final: 0.6851 (mmt) REVERT: B 892 LEU cc_start: 0.9318 (mp) cc_final: 0.9012 (mp) REVERT: B 1975 MET cc_start: 0.7982 (ptt) cc_final: 0.7724 (ptp) REVERT: B 2468 MET cc_start: 0.9079 (mmt) cc_final: 0.8847 (mmt) REVERT: B 2585 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8200 (ppp) REVERT: B 2702 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.6614 (p0) REVERT: B 2721 ILE cc_start: 0.9556 (mt) cc_final: 0.9215 (mm) REVERT: B 2828 MET cc_start: 0.7408 (tpt) cc_final: 0.6828 (tpp) REVERT: B 2867 ASN cc_start: -0.1164 (OUTLIER) cc_final: -0.2865 (m-40) REVERT: B 2897 GLN cc_start: 0.8818 (mm110) cc_final: 0.8588 (tm-30) REVERT: B 2943 PHE cc_start: 0.7900 (m-80) cc_final: 0.7256 (t80) REVERT: B 3068 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8363 (tt) REVERT: B 3211 LEU cc_start: 0.8892 (tp) cc_final: 0.8684 (pt) REVERT: B 3235 MET cc_start: 0.7349 (mtt) cc_final: 0.7023 (mtt) REVERT: B 3242 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8875 (pp) REVERT: B 3243 CYS cc_start: 0.8904 (m) cc_final: 0.8057 (m) REVERT: B 3246 MET cc_start: 0.8904 (ttp) cc_final: 0.8649 (ttp) REVERT: B 3250 TRP cc_start: 0.9383 (t60) cc_final: 0.9178 (t60) REVERT: B 3295 TRP cc_start: 0.8781 (p-90) cc_final: 0.8253 (p-90) REVERT: B 3299 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 3605 MET cc_start: 0.2317 (OUTLIER) cc_final: -0.0337 (tpp) REVERT: B 3719 MET cc_start: 0.8043 (tpp) cc_final: 0.7769 (tpp) REVERT: C 309 MET cc_start: 0.7037 (mmp) cc_final: 0.6745 (mmp) REVERT: C 935 MET cc_start: 0.8702 (tmm) cc_final: 0.8313 (tmm) REVERT: C 995 MET cc_start: 0.8500 (tmm) cc_final: 0.8147 (tmt) REVERT: C 1035 TYR cc_start: 0.8488 (t80) cc_final: 0.8230 (t80) REVERT: C 1064 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7355 (pp) REVERT: C 2066 MET cc_start: 0.8530 (mmp) cc_final: 0.8122 (mmt) REVERT: C 2192 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7492 (tpt) REVERT: C 2585 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7908 (pp-130) REVERT: C 2607 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 2771 TYR cc_start: 0.8631 (m-80) cc_final: 0.8281 (m-80) REVERT: C 2850 ASN cc_start: 0.9215 (t0) cc_final: 0.8617 (t0) REVERT: C 2880 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8639 (mppt) REVERT: C 2884 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8274 (tmtm) REVERT: C 2923 TYR cc_start: 0.8216 (t80) cc_final: 0.7784 (t80) REVERT: C 2943 PHE cc_start: 0.7733 (m-80) cc_final: 0.7323 (m-10) REVERT: C 3105 LEU cc_start: 0.8424 (mt) cc_final: 0.8204 (tt) REVERT: C 3131 TYR cc_start: 0.8757 (m-10) cc_final: 0.8520 (m-80) REVERT: C 3178 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.7004 (m90) REVERT: C 3200 ASN cc_start: 0.7149 (t0) cc_final: 0.6862 (t0) REVERT: C 3220 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8104 (tp30) REVERT: C 3235 MET cc_start: 0.6784 (mtt) cc_final: 0.6288 (mtp) REVERT: C 3242 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8907 (pp) REVERT: C 3246 MET cc_start: 0.8904 (ttp) cc_final: 0.8456 (ttm) REVERT: C 3295 TRP cc_start: 0.8658 (p-90) cc_final: 0.8289 (p-90) REVERT: C 3296 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8276 (mpt) REVERT: C 3299 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8243 (tt) REVERT: C 3605 MET cc_start: 0.2582 (OUTLIER) cc_final: 0.0355 (mpp) REVERT: C 3719 MET cc_start: 0.7922 (tpp) cc_final: 0.7669 (tpp) REVERT: J 13 PHE cc_start: 0.8744 (m-80) cc_final: 0.7916 (m-80) REVERT: J 64 ILE cc_start: 0.7953 (mm) cc_final: 0.7710 (tt) REVERT: J 69 PHE cc_start: 0.8716 (t80) cc_final: 0.8200 (t80) REVERT: J 125 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6049 (mtm) REVERT: J 138 ASN cc_start: 0.7365 (t0) cc_final: 0.7118 (t0) REVERT: J 145 MET cc_start: 0.1357 (pmm) cc_final: 0.0864 (pmm) REVERT: J 146 MET cc_start: -0.0803 (ptt) cc_final: -0.1790 (ppp) REVERT: K 43 ASN cc_start: 0.8449 (t0) cc_final: 0.8188 (t0) REVERT: K 64 ILE cc_start: 0.8050 (mm) cc_final: 0.7761 (tt) REVERT: K 125 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6814 (mpp) REVERT: K 145 MET cc_start: 0.2380 (pmm) cc_final: 0.1843 (pmm) REVERT: K 146 MET cc_start: 0.0018 (ptt) cc_final: -0.0580 (ppp) REVERT: L 43 ASN cc_start: 0.8470 (t0) cc_final: 0.8149 (t0) REVERT: L 106 LEU cc_start: 0.7946 (mt) cc_final: 0.7661 (tm) REVERT: L 146 MET cc_start: 0.0090 (ptt) cc_final: -0.0264 (pmm) outliers start: 288 outliers final: 40 residues processed: 1276 average time/residue: 2.0632 time to fit residues: 3820.7612 Evaluate side-chains 1091 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1016 time to evaluate : 12.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2214 MET Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2659 GLN Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2702 ASN Chi-restraints excluded: chain A residue 2844 MET Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 2983 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3123 LEU Chi-restraints excluded: chain A residue 3218 ILE Chi-restraints excluded: chain A residue 3242 LEU Chi-restraints excluded: chain A residue 3299 LEU Chi-restraints excluded: chain A residue 3605 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2659 GLN Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2702 ASN Chi-restraints excluded: chain D residue 2782 MET Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 2896 LEU Chi-restraints excluded: chain D residue 2938 GLN Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3123 LEU Chi-restraints excluded: chain D residue 3218 ILE Chi-restraints excluded: chain D residue 3242 LEU Chi-restraints excluded: chain D residue 3605 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 2585 MET Chi-restraints excluded: chain B residue 2659 GLN Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain B residue 2772 ARG Chi-restraints excluded: chain B residue 2844 MET Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2938 GLN Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3123 LEU Chi-restraints excluded: chain B residue 3242 LEU Chi-restraints excluded: chain B residue 3299 LEU Chi-restraints excluded: chain B residue 3605 MET Chi-restraints excluded: chain C residue 1064 LEU Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2607 LEU Chi-restraints excluded: chain C residue 2659 GLN Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2704 GLN Chi-restraints excluded: chain C residue 2772 ARG Chi-restraints excluded: chain C residue 2833 LEU Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 2880 LYS Chi-restraints excluded: chain C residue 2884 LYS Chi-restraints excluded: chain C residue 2938 GLN Chi-restraints excluded: chain C residue 3123 LEU Chi-restraints excluded: chain C residue 3178 HIS Chi-restraints excluded: chain C residue 3184 TYR Chi-restraints excluded: chain C residue 3242 LEU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3605 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1506 optimal weight: 6.9990 chunk 1352 optimal weight: 0.7980 chunk 750 optimal weight: 40.0000 chunk 461 optimal weight: 9.9990 chunk 912 optimal weight: 20.0000 chunk 722 optimal weight: 20.0000 chunk 1398 optimal weight: 3.9990 chunk 541 optimal weight: 9.9990 chunk 850 optimal weight: 0.9990 chunk 1040 optimal weight: 9.9990 chunk 1620 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2224 ASN A2700 ASN ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3031 ASN A3272 HIS A3964 GLN A4049 HIS A4267 GLN ** A4936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1844 GLN ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1974 ASN ** D2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2684 ASN D2700 ASN D2867 ASN D3031 ASN D3233 HIS D3964 GLN D4049 HIS D4267 GLN D4579 HIS ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 692 HIS B1593 HIS B1844 GLN ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1974 ASN B2684 ASN B2847 ASN ** B2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3031 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS B3252 HIS B3964 GLN B4049 HIS B4267 GLN ** B4936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 261 HIS C 651 HIS ** C1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1844 GLN C1974 ASN C3031 ASN C3034 HIS C3178 HIS C3230 GLN C3964 GLN C4049 HIS C4936 GLN J 9 GLN ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 146296 Z= 0.364 Angle : 0.706 17.551 197604 Z= 0.361 Chirality : 0.045 0.204 21684 Planarity : 0.006 0.142 25424 Dihedral : 6.725 89.723 19839 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 1.21 % Allowed : 5.96 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.32 (0.06), residues: 17776 helix: 1.00 (0.06), residues: 9012 sheet: -0.33 (0.12), residues: 1836 loop : -0.57 (0.07), residues: 6928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1156 HIS 0.019 0.002 HIS G 26 PHE 0.045 0.003 PHE C1979 TYR 0.042 0.002 TYR D2801 ARG 0.016 0.001 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1145 time to evaluate : 12.408 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: A 198 ASN cc_start: 0.7526 (p0) cc_final: 0.7326 (p0) REVERT: A 309 MET cc_start: 0.6939 (mmp) cc_final: 0.6606 (mpm) REVERT: A 545 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7639 (tpp80) REVERT: A 1948 MET cc_start: 0.7254 (mmp) cc_final: 0.6843 (mmp) REVERT: A 2142 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7104 (ttp) REVERT: A 2584 MET cc_start: 0.8942 (tpp) cc_final: 0.8448 (ttt) REVERT: A 2585 MET cc_start: 0.7925 (pmm) cc_final: 0.7622 (pp-130) REVERT: A 2689 MET cc_start: 0.1849 (OUTLIER) cc_final: -0.0809 (ttt) REVERT: A 2719 TYR cc_start: 0.8348 (t80) cc_final: 0.7979 (t80) REVERT: A 2724 TYR cc_start: 0.8932 (t80) cc_final: 0.7730 (t80) REVERT: A 2850 ASN cc_start: 0.9331 (t0) cc_final: 0.8721 (t0) REVERT: A 2867 ASN cc_start: 0.1073 (OUTLIER) cc_final: 0.0861 (p0) REVERT: A 2923 TYR cc_start: 0.8261 (t80) cc_final: 0.8024 (t80) REVERT: A 3043 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7498 (mmp80) REVERT: A 3046 MET cc_start: 0.7788 (mmt) cc_final: 0.7419 (mpm) REVERT: A 3072 MET cc_start: 0.8465 (mmt) cc_final: 0.8102 (mmt) REVERT: A 3075 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7996 (tt) REVERT: A 3101 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7809 (mm) REVERT: A 3117 PHE cc_start: 0.8683 (m-10) cc_final: 0.8322 (m-80) REVERT: A 3121 LEU cc_start: 0.8845 (tm) cc_final: 0.8434 (mt) REVERT: A 3159 LEU cc_start: 0.8727 (mt) cc_final: 0.8450 (mp) REVERT: A 3295 TRP cc_start: 0.8818 (p-90) cc_final: 0.8271 (p-90) REVERT: A 3298 ARG cc_start: 0.8406 (ptt90) cc_final: 0.7896 (ppt-90) REVERT: A 3323 MET cc_start: 0.7577 (mmp) cc_final: 0.7374 (mmm) REVERT: A 3605 MET cc_start: 0.3026 (tmm) cc_final: 0.1801 (tpp) REVERT: A 3981 MET cc_start: 0.8661 (tmm) cc_final: 0.8444 (ttp) REVERT: A 4268 MET cc_start: 0.5584 (mmm) cc_final: 0.5340 (ttm) REVERT: A 4707 MET cc_start: 0.8303 (ttp) cc_final: 0.7992 (ttm) REVERT: E 53 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8843 (ttmp) REVERT: F 53 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8786 (ttmp) REVERT: F 58 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8056 (mtmp) REVERT: G 54 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: I 1 MET cc_start: 0.6688 (mmt) cc_final: 0.6463 (mmt) REVERT: I 52 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8238 (ptt) REVERT: I 73 MET cc_start: 0.7951 (ppp) cc_final: 0.7712 (pp-130) REVERT: I 145 MET cc_start: 0.2799 (pmm) cc_final: 0.2513 (pmt) REVERT: D 241 MET cc_start: 0.5660 (mmp) cc_final: 0.5396 (mmt) REVERT: D 317 MET cc_start: 0.7617 (ptt) cc_final: 0.7315 (ptt) REVERT: D 399 MET cc_start: 0.7787 (pmm) cc_final: 0.7284 (tmm) REVERT: D 885 LEU cc_start: 0.9566 (mt) cc_final: 0.9334 (mm) REVERT: D 935 MET cc_start: 0.8429 (ptm) cc_final: 0.8037 (ptm) REVERT: D 940 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9107 (pt) REVERT: D 964 MET cc_start: 0.3515 (OUTLIER) cc_final: 0.3122 (pmm) REVERT: D 1165 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8004 (mtp) REVERT: D 1300 MET cc_start: 0.8527 (mmm) cc_final: 0.8285 (mmt) REVERT: D 1494 MET cc_start: 0.8380 (ppp) cc_final: 0.8178 (ppp) REVERT: D 1599 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: D 1975 MET cc_start: 0.8086 (ptp) cc_final: 0.7824 (ptp) REVERT: D 2666 LEU cc_start: 0.9053 (tt) cc_final: 0.8746 (pp) REVERT: D 2688 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4100 (ptm) REVERT: D 2719 TYR cc_start: 0.8503 (t80) cc_final: 0.8107 (t80) REVERT: D 2734 MET cc_start: 0.7411 (mpt) cc_final: 0.6977 (mpt) REVERT: D 2785 TRP cc_start: 0.7743 (m-10) cc_final: 0.7451 (m-10) REVERT: D 2828 MET cc_start: 0.7241 (tpp) cc_final: 0.6550 (mmt) REVERT: D 2840 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7979 (mmm) REVERT: D 2870 LEU cc_start: 0.8838 (mt) cc_final: 0.8514 (mm) REVERT: D 2895 PHE cc_start: 0.9023 (t80) cc_final: 0.8799 (t80) REVERT: D 3074 ASN cc_start: 0.8349 (p0) cc_final: 0.8089 (p0) REVERT: D 3131 TYR cc_start: 0.8439 (m-10) cc_final: 0.8225 (m-80) REVERT: D 3211 LEU cc_start: 0.9084 (tp) cc_final: 0.8761 (pt) REVERT: D 3233 HIS cc_start: 0.8012 (t70) cc_final: 0.7809 (t-90) REVERT: D 3235 MET cc_start: 0.7158 (mtt) cc_final: 0.6361 (tpp) REVERT: D 3250 TRP cc_start: 0.9288 (t60) cc_final: 0.8832 (t-100) REVERT: D 3268 LEU cc_start: 0.7729 (mt) cc_final: 0.7260 (pt) REVERT: D 3295 TRP cc_start: 0.8989 (p-90) cc_final: 0.8744 (p-90) REVERT: D 3605 MET cc_start: 0.3057 (tmm) cc_final: 0.2192 (tpt) REVERT: D 3954 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: D 4274 MET cc_start: 0.6217 (tmm) cc_final: 0.6016 (tmm) REVERT: B 309 MET cc_start: 0.7266 (mmp) cc_final: 0.6977 (mmm) REVERT: B 1721 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: B 1948 MET cc_start: 0.7449 (mmp) cc_final: 0.7117 (mmt) REVERT: B 2142 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7449 (ttt) REVERT: B 2721 ILE cc_start: 0.9540 (mt) cc_final: 0.9271 (mm) REVERT: B 2724 TYR cc_start: 0.8930 (t80) cc_final: 0.8475 (t80) REVERT: B 2760 TYR cc_start: 0.7602 (t80) cc_final: 0.7389 (t80) REVERT: B 2772 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8585 (pmm-80) REVERT: B 2828 MET cc_start: 0.7420 (tpt) cc_final: 0.7143 (mmt) REVERT: B 2844 MET cc_start: 0.8931 (ppp) cc_final: 0.8642 (ppp) REVERT: B 2867 ASN cc_start: -0.0751 (OUTLIER) cc_final: -0.2439 (m-40) REVERT: B 2880 LYS cc_start: 0.8910 (mppt) cc_final: 0.8639 (mppt) REVERT: B 2884 LYS cc_start: 0.8989 (mppt) cc_final: 0.8651 (tmtm) REVERT: B 2886 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8732 (mmt-90) REVERT: B 2895 PHE cc_start: 0.9172 (t80) cc_final: 0.8928 (t80) REVERT: B 2939 TYR cc_start: 0.7895 (m-80) cc_final: 0.7388 (m-80) REVERT: B 2941 LEU cc_start: 0.9081 (pp) cc_final: 0.8731 (mm) REVERT: B 3068 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 3233 HIS cc_start: 0.8242 (t70) cc_final: 0.8017 (t-90) REVERT: B 3235 MET cc_start: 0.7616 (mtt) cc_final: 0.7081 (mtp) REVERT: B 3242 LEU cc_start: 0.9394 (mt) cc_final: 0.9133 (pp) REVERT: B 3243 CYS cc_start: 0.8861 (m) cc_final: 0.8434 (p) REVERT: B 3250 TRP cc_start: 0.9412 (t60) cc_final: 0.9200 (t60) REVERT: B 3295 TRP cc_start: 0.9051 (p-90) cc_final: 0.8620 (p-90) REVERT: B 3299 LEU cc_start: 0.8773 (mt) cc_final: 0.8532 (mt) REVERT: B 3689 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (mpp) REVERT: B 4256 MET cc_start: 0.8301 (mtp) cc_final: 0.8095 (mtp) REVERT: C 309 MET cc_start: 0.7151 (mmp) cc_final: 0.6939 (mmm) REVERT: C 865 ILE cc_start: 0.9313 (mm) cc_final: 0.9107 (tp) REVERT: C 935 MET cc_start: 0.8663 (tmm) cc_final: 0.8298 (tmm) REVERT: C 1035 TYR cc_start: 0.8608 (t80) cc_final: 0.8321 (t80) REVERT: C 1165 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7851 (mtp) REVERT: C 2389 MET cc_start: 0.8102 (mtt) cc_final: 0.7786 (mtt) REVERT: C 2585 MET cc_start: 0.7724 (pmm) cc_final: 0.7309 (pp-130) REVERT: C 2605 MET cc_start: 0.8987 (tmm) cc_final: 0.8716 (tmm) REVERT: C 2729 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8664 (t-170) REVERT: C 2772 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8834 (pmm-80) REVERT: C 2798 MET cc_start: 0.8290 (mmm) cc_final: 0.7986 (ptp) REVERT: C 2844 MET cc_start: 0.8776 (ppp) cc_final: 0.8454 (ppp) REVERT: C 2850 ASN cc_start: 0.9159 (t0) cc_final: 0.8606 (t0) REVERT: C 2885 ASP cc_start: 0.8802 (m-30) cc_final: 0.8591 (m-30) REVERT: C 2886 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8376 (mmt-90) REVERT: C 2923 TYR cc_start: 0.8272 (t80) cc_final: 0.7870 (t80) REVERT: C 2939 TYR cc_start: 0.7883 (m-80) cc_final: 0.7327 (m-80) REVERT: C 2943 PHE cc_start: 0.7849 (m-80) cc_final: 0.7420 (m-10) REVERT: C 2956 TYR cc_start: 0.8452 (m-80) cc_final: 0.8225 (m-10) REVERT: C 3109 PHE cc_start: 0.8374 (m-80) cc_final: 0.7899 (m-80) REVERT: C 3121 LEU cc_start: 0.8703 (tp) cc_final: 0.8420 (mt) REVERT: C 3131 TYR cc_start: 0.8817 (m-10) cc_final: 0.8419 (m-80) REVERT: C 3200 ASN cc_start: 0.7402 (t0) cc_final: 0.6960 (t0) REVERT: C 3220 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8080 (tp30) REVERT: C 3233 HIS cc_start: 0.7781 (t-90) cc_final: 0.7562 (t-90) REVERT: C 3235 MET cc_start: 0.7140 (mtt) cc_final: 0.6752 (mtp) REVERT: C 3242 LEU cc_start: 0.9300 (mt) cc_final: 0.8820 (pp) REVERT: C 3296 MET cc_start: 0.8551 (mtm) cc_final: 0.8069 (mmt) REVERT: C 3689 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7934 (mtt) REVERT: C 4256 MET cc_start: 0.8236 (mtp) cc_final: 0.8006 (mtp) REVERT: J 9 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8506 (pp30) REVERT: J 13 PHE cc_start: 0.8622 (m-80) cc_final: 0.8008 (m-80) REVERT: J 50 GLN cc_start: 0.9218 (pm20) cc_final: 0.8786 (tm-30) REVERT: J 64 ILE cc_start: 0.8236 (mm) cc_final: 0.7908 (tt) REVERT: J 69 PHE cc_start: 0.8282 (t80) cc_final: 0.8054 (t80) REVERT: J 138 ASN cc_start: 0.7480 (t0) cc_final: 0.6967 (t0) REVERT: J 145 MET cc_start: 0.0807 (pmm) cc_final: 0.0233 (pmm) REVERT: J 146 MET cc_start: -0.0915 (ptt) cc_final: -0.1814 (pp-130) REVERT: K 50 GLN cc_start: 0.9117 (pm20) cc_final: 0.8619 (tm-30) REVERT: K 145 MET cc_start: 0.1880 (pmm) cc_final: 0.1328 (pmm) REVERT: K 146 MET cc_start: 0.0178 (ptt) cc_final: -0.0117 (pmt) REVERT: L 1 MET cc_start: 0.6749 (mmt) cc_final: 0.6305 (mmp) REVERT: L 9 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: L 73 MET cc_start: 0.8076 (ppp) cc_final: 0.7785 (pp-130) REVERT: L 146 MET cc_start: -0.0203 (ptt) cc_final: -0.0608 (pmm) outliers start: 182 outliers final: 36 residues processed: 1194 average time/residue: 2.0137 time to fit residues: 3520.7707 Evaluate side-chains 1135 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1071 time to evaluate : 12.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 2142 MET Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 2983 LEU Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3115 HIS Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 2688 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2840 MET Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1501 ASN Chi-restraints excluded: chain B residue 1721 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2772 ARG Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2870 LEU Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2729 HIS Chi-restraints excluded: chain C residue 2772 ARG Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2886 ARG Chi-restraints excluded: chain C residue 3003 MET Chi-restraints excluded: chain C residue 3034 HIS Chi-restraints excluded: chain C residue 3184 TYR Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain C residue 4305 PHE Chi-restraints excluded: chain J residue 9 GLN Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 900 optimal weight: 5.9990 chunk 502 optimal weight: 5.9990 chunk 1348 optimal weight: 9.9990 chunk 1103 optimal weight: 0.9980 chunk 446 optimal weight: 0.0570 chunk 1622 optimal weight: 8.9990 chunk 1753 optimal weight: 0.0770 chunk 1445 optimal weight: 4.9990 chunk 1609 optimal weight: 30.0000 chunk 553 optimal weight: 0.2980 chunk 1302 optimal weight: 3.9990 overall best weight: 1.0858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 GLN ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2089 HIS A2224 ASN A3304 GLN ** A4936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS D1593 HIS ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2684 ASN D2867 ASN D3151 GLN D3252 HIS D4933 HIS ** D4936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 692 HIS B1593 HIS ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN B3115 HIS B3151 GLN B3252 HIS B3304 GLN B4936 GLN C1477 HIS C1501 ASN C1593 HIS C2995 HIS C3034 HIS C3115 HIS C3151 GLN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 146296 Z= 0.167 Angle : 0.583 17.820 197604 Z= 0.294 Chirality : 0.040 0.212 21684 Planarity : 0.004 0.136 25424 Dihedral : 5.750 76.419 19672 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 0.88 % Allowed : 7.74 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.06), residues: 17776 helix: 1.33 (0.06), residues: 9036 sheet: -0.04 (0.13), residues: 1608 loop : -0.52 (0.07), residues: 7132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D2852 HIS 0.023 0.001 HIS C3034 PHE 0.033 0.001 PHE C1979 TYR 0.037 0.001 TYR D3245 ARG 0.015 0.000 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1093 time to evaluate : 12.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 26 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8411 (t-90) REVERT: A 198 ASN cc_start: 0.7418 (p0) cc_final: 0.7154 (p0) REVERT: A 892 LEU cc_start: 0.9245 (mm) cc_final: 0.8948 (mt) REVERT: A 1494 MET cc_start: 0.8312 (ppp) cc_final: 0.8058 (ppp) REVERT: A 1948 MET cc_start: 0.7264 (mmp) cc_final: 0.6865 (mmt) REVERT: A 2066 MET cc_start: 0.8910 (mmp) cc_final: 0.8543 (mmp) REVERT: A 2584 MET cc_start: 0.8943 (tpp) cc_final: 0.8676 (ttt) REVERT: A 2585 MET cc_start: 0.7871 (pmm) cc_final: 0.7393 (pp-130) REVERT: A 2689 MET cc_start: 0.1870 (ptt) cc_final: -0.0678 (ttt) REVERT: A 2724 TYR cc_start: 0.8900 (t80) cc_final: 0.8303 (t80) REVERT: A 2850 ASN cc_start: 0.9264 (m-40) cc_final: 0.8578 (t0) REVERT: A 2867 ASN cc_start: 0.1110 (OUTLIER) cc_final: 0.0867 (p0) REVERT: A 2923 TYR cc_start: 0.8192 (t80) cc_final: 0.7984 (t80) REVERT: A 3117 PHE cc_start: 0.8568 (m-10) cc_final: 0.8286 (m-80) REVERT: A 3121 LEU cc_start: 0.8832 (tm) cc_final: 0.8432 (mt) REVERT: A 3123 LEU cc_start: 0.8916 (mt) cc_final: 0.8544 (mm) REVERT: A 3298 ARG cc_start: 0.8434 (ptt90) cc_final: 0.8092 (mtm110) REVERT: A 3605 MET cc_start: 0.3125 (tmm) cc_final: 0.1900 (tpp) REVERT: A 3819 MET cc_start: 0.6660 (mpp) cc_final: 0.6377 (mtm) REVERT: A 3981 MET cc_start: 0.8710 (tmm) cc_final: 0.8492 (ttp) REVERT: A 4035 TYR cc_start: 0.7673 (m-80) cc_final: 0.7425 (m-80) REVERT: A 4268 MET cc_start: 0.5591 (mmm) cc_final: 0.5359 (ttm) REVERT: A 4568 MET cc_start: 0.7893 (mmm) cc_final: 0.7567 (mmt) REVERT: F 26 HIS cc_start: 0.9165 (OUTLIER) cc_final: 0.8440 (t-90) REVERT: G 26 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8465 (t-90) REVERT: G 53 LYS cc_start: 0.8925 (tppt) cc_final: 0.8657 (tttt) REVERT: I 64 ILE cc_start: 0.8222 (mm) cc_final: 0.8009 (tt) REVERT: I 72 MET cc_start: 0.7130 (tpp) cc_final: 0.6900 (tpt) REVERT: I 73 MET cc_start: 0.8019 (ppp) cc_final: 0.7734 (pp-130) REVERT: I 142 PHE cc_start: 0.7000 (t80) cc_final: 0.6723 (t80) REVERT: I 146 MET cc_start: 0.0265 (ptt) cc_final: -0.0424 (pmm) REVERT: D 241 MET cc_start: 0.5587 (mmp) cc_final: 0.5235 (mmt) REVERT: D 317 MET cc_start: 0.7602 (ptt) cc_final: 0.7324 (ptt) REVERT: D 393 MET cc_start: 0.6905 (mmm) cc_final: 0.6495 (mmm) REVERT: D 399 MET cc_start: 0.7804 (pmm) cc_final: 0.7299 (tmm) REVERT: D 885 LEU cc_start: 0.9575 (mt) cc_final: 0.9336 (mm) REVERT: D 931 TYR cc_start: 0.7515 (t80) cc_final: 0.7305 (t80) REVERT: D 935 MET cc_start: 0.8337 (ptm) cc_final: 0.7972 (ptm) REVERT: D 1165 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7989 (mtp) REVERT: D 1300 MET cc_start: 0.8511 (mmm) cc_final: 0.8254 (mmp) REVERT: D 1494 MET cc_start: 0.8412 (ppp) cc_final: 0.8156 (ppp) REVERT: D 1975 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7841 (ptp) REVERT: D 2384 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: D 2456 MET cc_start: 0.8670 (mmm) cc_final: 0.8421 (tpp) REVERT: D 2666 LEU cc_start: 0.9026 (tt) cc_final: 0.8759 (pp) REVERT: D 2719 TYR cc_start: 0.8406 (t80) cc_final: 0.8027 (t80) REVERT: D 2828 MET cc_start: 0.7440 (tpp) cc_final: 0.6687 (mmm) REVERT: D 2844 MET cc_start: 0.9046 (ppp) cc_final: 0.8735 (ppp) REVERT: D 2870 LEU cc_start: 0.8828 (mt) cc_final: 0.8534 (OUTLIER) REVERT: D 2895 PHE cc_start: 0.9114 (t80) cc_final: 0.8781 (t80) REVERT: D 2983 LEU cc_start: 0.8601 (mm) cc_final: 0.8389 (mm) REVERT: D 3046 MET cc_start: 0.8193 (mmt) cc_final: 0.7974 (mmm) REVERT: D 3072 MET cc_start: 0.8520 (mmt) cc_final: 0.8176 (mtm) REVERT: D 3115 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7568 (m90) REVERT: D 3211 LEU cc_start: 0.8988 (tp) cc_final: 0.8632 (pt) REVERT: D 3233 HIS cc_start: 0.7992 (t70) cc_final: 0.7768 (t-90) REVERT: D 3954 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: B 1948 MET cc_start: 0.7495 (mmp) cc_final: 0.7161 (mmt) REVERT: B 1975 MET cc_start: 0.8380 (ptp) cc_final: 0.7985 (ptp) REVERT: B 2066 MET cc_start: 0.9056 (mmp) cc_final: 0.8778 (mmt) REVERT: B 2347 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: B 2468 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8793 (mpp) REVERT: B 2721 ILE cc_start: 0.9510 (mt) cc_final: 0.9293 (mm) REVERT: B 2724 TYR cc_start: 0.8999 (t80) cc_final: 0.8437 (t80) REVERT: B 2734 MET cc_start: 0.8134 (mpt) cc_final: 0.7732 (mpt) REVERT: B 2771 TYR cc_start: 0.8716 (m-80) cc_final: 0.8466 (m-80) REVERT: B 2828 MET cc_start: 0.7437 (tpt) cc_final: 0.6998 (mmt) REVERT: B 2840 MET cc_start: 0.8315 (mmt) cc_final: 0.7841 (tpt) REVERT: B 2867 ASN cc_start: -0.0338 (OUTLIER) cc_final: -0.2089 (m-40) REVERT: B 2880 LYS cc_start: 0.8880 (mppt) cc_final: 0.8560 (mppt) REVERT: B 2884 LYS cc_start: 0.8957 (mppt) cc_final: 0.8641 (tmtt) REVERT: B 2886 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8890 (mmm-85) REVERT: B 2895 PHE cc_start: 0.9217 (t80) cc_final: 0.8821 (t80) REVERT: B 2939 TYR cc_start: 0.7875 (m-80) cc_final: 0.7349 (m-80) REVERT: B 3046 MET cc_start: 0.8208 (mmm) cc_final: 0.7905 (mmm) REVERT: B 3068 LEU cc_start: 0.8715 (tp) cc_final: 0.8303 (mt) REVERT: B 3214 LEU cc_start: 0.9204 (mp) cc_final: 0.8956 (mm) REVERT: B 3235 MET cc_start: 0.7776 (mtt) cc_final: 0.7269 (mtp) REVERT: B 3242 LEU cc_start: 0.9355 (mt) cc_final: 0.9064 (pp) REVERT: B 3243 CYS cc_start: 0.8820 (m) cc_final: 0.8397 (p) REVERT: B 3250 TRP cc_start: 0.9395 (t60) cc_final: 0.9171 (t60) REVERT: B 3295 TRP cc_start: 0.9007 (p-90) cc_final: 0.8703 (p-90) REVERT: C 885 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9211 (mm) REVERT: C 935 MET cc_start: 0.8743 (tmm) cc_final: 0.8358 (tmm) REVERT: C 1035 TYR cc_start: 0.8567 (t80) cc_final: 0.8315 (t80) REVERT: C 1165 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: C 1599 MET cc_start: 0.8585 (tpp) cc_final: 0.8336 (ttp) REVERT: C 2066 MET cc_start: 0.8927 (mmp) cc_final: 0.8713 (mmp) REVERT: C 2347 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7871 (mtm) REVERT: C 2731 LYS cc_start: 0.9279 (ptpp) cc_final: 0.9050 (pttt) REVERT: C 2734 MET cc_start: 0.8250 (mpt) cc_final: 0.7882 (mpt) REVERT: C 2798 MET cc_start: 0.8141 (mmm) cc_final: 0.7694 (ptp) REVERT: C 2848 TYR cc_start: 0.8620 (t80) cc_final: 0.8377 (t80) REVERT: C 2850 ASN cc_start: 0.9191 (t0) cc_final: 0.8570 (t0) REVERT: C 2884 LYS cc_start: 0.9335 (mmpt) cc_final: 0.8890 (tmtm) REVERT: C 2923 TYR cc_start: 0.8250 (t80) cc_final: 0.7826 (t80) REVERT: C 2939 TYR cc_start: 0.7868 (m-80) cc_final: 0.7214 (m-80) REVERT: C 2943 PHE cc_start: 0.7870 (m-80) cc_final: 0.7352 (m-10) REVERT: C 2956 TYR cc_start: 0.8392 (m-80) cc_final: 0.8178 (m-10) REVERT: C 2980 LEU cc_start: 0.8802 (mm) cc_final: 0.8574 (mm) REVERT: C 3109 PHE cc_start: 0.8333 (m-80) cc_final: 0.7950 (m-80) REVERT: C 3121 LEU cc_start: 0.8701 (tp) cc_final: 0.8378 (mt) REVERT: C 3131 TYR cc_start: 0.8789 (m-10) cc_final: 0.8407 (m-80) REVERT: C 3233 HIS cc_start: 0.7701 (t-90) cc_final: 0.7489 (t-90) REVERT: C 3235 MET cc_start: 0.7043 (mtt) cc_final: 0.6623 (mtp) REVERT: C 3242 LEU cc_start: 0.9238 (mt) cc_final: 0.8811 (pp) REVERT: C 3719 MET cc_start: 0.7729 (tpp) cc_final: 0.7497 (mmm) REVERT: C 4256 MET cc_start: 0.8201 (mtp) cc_final: 0.7981 (mtp) REVERT: J 13 PHE cc_start: 0.8760 (m-80) cc_final: 0.8513 (m-80) REVERT: J 64 ILE cc_start: 0.8223 (mm) cc_final: 0.7917 (tt) REVERT: J 69 PHE cc_start: 0.8207 (t80) cc_final: 0.7991 (t80) REVERT: J 138 ASN cc_start: 0.7593 (t0) cc_final: 0.6969 (t0) REVERT: J 145 MET cc_start: 0.0864 (pmm) cc_final: 0.0367 (pmm) REVERT: J 146 MET cc_start: -0.1110 (ptt) cc_final: -0.1895 (pp-130) REVERT: K 13 PHE cc_start: 0.8524 (m-80) cc_final: 0.8185 (m-80) REVERT: K 69 PHE cc_start: 0.8210 (t80) cc_final: 0.8005 (t80) REVERT: K 73 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8004 (pp-130) REVERT: K 145 MET cc_start: 0.1578 (pmm) cc_final: 0.0990 (pmm) REVERT: K 146 MET cc_start: 0.0208 (ptt) cc_final: -0.0193 (pmt) REVERT: L 1 MET cc_start: 0.6783 (mmt) cc_final: 0.6460 (mmt) outliers start: 130 outliers final: 35 residues processed: 1136 average time/residue: 2.0018 time to fit residues: 3316.0854 Evaluate side-chains 1103 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1053 time to evaluate : 11.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 2983 LEU Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 3115 HIS Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2384 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2598 LEU Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3123 LEU Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1501 ASN Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2468 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3123 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 3034 HIS Chi-restraints excluded: chain C residue 3123 LEU Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 18 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1603 optimal weight: 30.0000 chunk 1220 optimal weight: 10.0000 chunk 842 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 774 optimal weight: 7.9990 chunk 1089 optimal weight: 9.9990 chunk 1628 optimal weight: 30.0000 chunk 1724 optimal weight: 0.6980 chunk 850 optimal weight: 10.0000 chunk 1543 optimal weight: 9.9990 chunk 464 optimal weight: 30.0000 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 915 HIS A1554 GLN A1844 GLN ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 HIS A2224 ASN A2684 ASN ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3230 GLN A4936 GLN D 33 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1554 GLN ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2217 HIS D2684 ASN D2867 ASN D3252 HIS D4579 HIS D4936 GLN B1554 GLN B1593 HIS ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN B2995 HIS B3252 HIS C1554 GLN C2217 HIS C2224 ASN C2847 ASN C3034 HIS C3115 HIS ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 146296 Z= 0.523 Angle : 0.697 16.022 197604 Z= 0.354 Chirality : 0.046 0.333 21684 Planarity : 0.005 0.139 25424 Dihedral : 5.774 79.004 19660 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 1.19 % Allowed : 8.57 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.57 (0.06), residues: 17776 helix: 1.26 (0.06), residues: 9120 sheet: -0.25 (0.12), residues: 1716 loop : -0.56 (0.07), residues: 6940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A2852 HIS 0.021 0.002 HIS C3034 PHE 0.041 0.002 PHE D1979 TYR 0.075 0.002 TYR D1703 ARG 0.016 0.001 ARG D1758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1125 time to evaluate : 12.445 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 198 ASN cc_start: 0.7573 (p0) cc_final: 0.7302 (p0) REVERT: A 317 MET cc_start: 0.7722 (ptt) cc_final: 0.7494 (ptt) REVERT: A 393 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6138 (mmm) REVERT: A 545 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7633 (tpp80) REVERT: A 892 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8999 (mt) REVERT: A 938 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: A 1035 TYR cc_start: 0.8776 (t80) cc_final: 0.8574 (t80) REVERT: A 1494 MET cc_start: 0.8418 (ppp) cc_final: 0.8181 (ppp) REVERT: A 1948 MET cc_start: 0.7236 (mmp) cc_final: 0.6852 (mmt) REVERT: A 1975 MET cc_start: 0.8267 (ptp) cc_final: 0.8015 (ptp) REVERT: A 2004 MET cc_start: 0.8750 (mmp) cc_final: 0.8549 (mmm) REVERT: A 2584 MET cc_start: 0.8981 (tpp) cc_final: 0.8733 (ttt) REVERT: A 2585 MET cc_start: 0.7818 (pmm) cc_final: 0.7519 (pmm) REVERT: A 2594 PHE cc_start: 0.8085 (m-80) cc_final: 0.7869 (m-80) REVERT: A 2662 PHE cc_start: 0.8648 (m-10) cc_final: 0.8237 (m-80) REVERT: A 2688 MET cc_start: 0.3352 (OUTLIER) cc_final: 0.2878 (pp-130) REVERT: A 2719 TYR cc_start: 0.8317 (t80) cc_final: 0.8016 (t80) REVERT: A 2724 TYR cc_start: 0.8930 (t80) cc_final: 0.7974 (t80) REVERT: A 2850 ASN cc_start: 0.9246 (m-40) cc_final: 0.8549 (t0) REVERT: A 2867 ASN cc_start: 0.1548 (OUTLIER) cc_final: 0.1336 (p0) REVERT: A 2895 PHE cc_start: 0.9201 (t80) cc_final: 0.8872 (t80) REVERT: A 2923 TYR cc_start: 0.8391 (t80) cc_final: 0.8147 (t80) REVERT: A 3046 MET cc_start: 0.8270 (mpp) cc_final: 0.7458 (mpp) REVERT: A 3123 LEU cc_start: 0.8931 (mt) cc_final: 0.8587 (mm) REVERT: A 3131 TYR cc_start: 0.8492 (m-10) cc_final: 0.8183 (m-80) REVERT: A 3159 LEU cc_start: 0.8820 (mt) cc_final: 0.8418 (mp) REVERT: A 3605 MET cc_start: 0.3105 (tmm) cc_final: 0.2324 (tpp) REVERT: A 3689 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: A 4035 TYR cc_start: 0.7821 (m-80) cc_final: 0.7479 (m-80) REVERT: A 4268 MET cc_start: 0.5598 (mmm) cc_final: 0.5315 (tpt) REVERT: F 26 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8662 (t-90) REVERT: F 58 LYS cc_start: 0.8378 (mtmp) cc_final: 0.8116 (ttpp) REVERT: F 67 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8524 (mtp) REVERT: I 52 MET cc_start: 0.8740 (ptt) cc_final: 0.8515 (ptt) REVERT: I 73 MET cc_start: 0.7897 (ppp) cc_final: 0.7696 (pp-130) REVERT: I 76 LYS cc_start: 0.8971 (ptpt) cc_final: 0.8642 (ptpt) REVERT: I 142 PHE cc_start: 0.6973 (t80) cc_final: 0.6753 (t80) REVERT: I 146 MET cc_start: 0.0504 (ptt) cc_final: -0.0172 (pmm) REVERT: D 198 ASN cc_start: 0.7791 (p0) cc_final: 0.7496 (p0) REVERT: D 317 MET cc_start: 0.7705 (ptt) cc_final: 0.7402 (ptt) REVERT: D 393 MET cc_start: 0.6673 (mmm) cc_final: 0.6125 (mmm) REVERT: D 399 MET cc_start: 0.7842 (pmm) cc_final: 0.7335 (tmm) REVERT: D 885 LEU cc_start: 0.9568 (mt) cc_final: 0.9333 (mm) REVERT: D 935 MET cc_start: 0.8445 (ptm) cc_final: 0.8047 (ptm) REVERT: D 940 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9163 (pt) REVERT: D 995 MET cc_start: 0.8242 (tmm) cc_final: 0.7868 (tpt) REVERT: D 1062 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.2949 (m-80) REVERT: D 1165 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7990 (mtp) REVERT: D 1300 MET cc_start: 0.8531 (mmm) cc_final: 0.8268 (mmp) REVERT: D 1494 MET cc_start: 0.8479 (ppp) cc_final: 0.8238 (ppp) REVERT: D 1599 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8363 (ttp) REVERT: D 1975 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8025 (ptp) REVERT: D 2279 MET cc_start: 0.8014 (ptm) cc_final: 0.7762 (ttp) REVERT: D 2605 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8450 (ttp) REVERT: D 2662 PHE cc_start: 0.8872 (m-80) cc_final: 0.8409 (m-80) REVERT: D 2666 LEU cc_start: 0.9187 (tt) cc_final: 0.8928 (pp) REVERT: D 2719 TYR cc_start: 0.8482 (t80) cc_final: 0.8074 (t80) REVERT: D 2724 TYR cc_start: 0.8836 (t80) cc_final: 0.8468 (t80) REVERT: D 2828 MET cc_start: 0.7447 (tpp) cc_final: 0.6768 (mmt) REVERT: D 2870 LEU cc_start: 0.8935 (mt) cc_final: 0.8662 (mm) REVERT: D 2895 PHE cc_start: 0.9190 (t80) cc_final: 0.8695 (t80) REVERT: D 3046 MET cc_start: 0.8252 (mmt) cc_final: 0.7960 (mmm) REVERT: D 3115 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7548 (m90) REVERT: D 3131 TYR cc_start: 0.8454 (m-10) cc_final: 0.8237 (m-80) REVERT: D 3211 LEU cc_start: 0.9103 (tp) cc_final: 0.8817 (pt) REVERT: D 3235 MET cc_start: 0.7547 (mtm) cc_final: 0.6760 (tpt) REVERT: D 3295 TRP cc_start: 0.8677 (p-90) cc_final: 0.8173 (p-90) REVERT: B 1842 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8803 (pp) REVERT: B 1948 MET cc_start: 0.7440 (mmp) cc_final: 0.7164 (mmt) REVERT: B 1975 MET cc_start: 0.8431 (ptp) cc_final: 0.8052 (ptp) REVERT: B 2347 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8534 (mtm) REVERT: B 2721 ILE cc_start: 0.9569 (mt) cc_final: 0.9361 (mm) REVERT: B 2724 TYR cc_start: 0.9044 (t80) cc_final: 0.8529 (t80) REVERT: B 2734 MET cc_start: 0.8247 (mpt) cc_final: 0.7696 (mpt) REVERT: B 2798 MET cc_start: 0.8874 (mmm) cc_final: 0.8426 (ptp) REVERT: B 2828 MET cc_start: 0.7588 (tpt) cc_final: 0.7095 (mmt) REVERT: B 2848 TYR cc_start: 0.8886 (t80) cc_final: 0.8648 (t80) REVERT: B 2867 ASN cc_start: -0.0072 (OUTLIER) cc_final: -0.0408 (p0) REVERT: B 2874 TYR cc_start: 0.8159 (t80) cc_final: 0.7830 (t80) REVERT: B 2880 LYS cc_start: 0.8938 (mppt) cc_final: 0.8635 (mppt) REVERT: B 2884 LYS cc_start: 0.8993 (mppt) cc_final: 0.8660 (tmtp) REVERT: B 2893 LEU cc_start: 0.9422 (mm) cc_final: 0.9170 (mp) REVERT: B 2895 PHE cc_start: 0.9254 (t80) cc_final: 0.8837 (t80) REVERT: B 2939 TYR cc_start: 0.7941 (m-80) cc_final: 0.7418 (m-80) REVERT: B 3046 MET cc_start: 0.8306 (mmm) cc_final: 0.7952 (mmm) REVERT: B 3068 LEU cc_start: 0.8844 (tp) cc_final: 0.8596 (tm) REVERT: B 3214 LEU cc_start: 0.9229 (mp) cc_final: 0.9016 (mt) REVERT: B 3233 HIS cc_start: 0.8323 (t-90) cc_final: 0.8083 (t-90) REVERT: B 3242 LEU cc_start: 0.9347 (mt) cc_final: 0.9014 (pp) REVERT: B 3243 CYS cc_start: 0.8871 (m) cc_final: 0.8052 (m) REVERT: B 3250 TRP cc_start: 0.9418 (t60) cc_final: 0.9170 (t60) REVERT: B 3295 TRP cc_start: 0.9007 (p-90) cc_final: 0.8622 (p-90) REVERT: B 3299 LEU cc_start: 0.8945 (mt) cc_final: 0.8613 (mt) REVERT: B 3689 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: B 4256 MET cc_start: 0.8310 (mtp) cc_final: 0.8096 (mtp) REVERT: C 935 MET cc_start: 0.8786 (tmm) cc_final: 0.8375 (tmm) REVERT: C 999 LEU cc_start: 0.9509 (tm) cc_final: 0.9303 (pp) REVERT: C 1035 TYR cc_start: 0.8725 (t80) cc_final: 0.8503 (t80) REVERT: C 1165 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7961 (mtp) REVERT: C 1948 MET cc_start: 0.7226 (mmp) cc_final: 0.6878 (mmt) REVERT: C 2347 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: C 2389 MET cc_start: 0.8389 (mtt) cc_final: 0.8139 (mtt) REVERT: C 2585 MET cc_start: 0.8076 (ppp) cc_final: 0.7838 (pmm) REVERT: C 2734 MET cc_start: 0.8129 (mpt) cc_final: 0.7552 (mpt) REVERT: C 2798 MET cc_start: 0.8399 (mmm) cc_final: 0.7580 (ptm) REVERT: C 2848 TYR cc_start: 0.8695 (t80) cc_final: 0.8441 (t80) REVERT: C 2850 ASN cc_start: 0.9159 (t0) cc_final: 0.8493 (t0) REVERT: C 2884 LYS cc_start: 0.9338 (mmpt) cc_final: 0.8875 (tmtm) REVERT: C 2923 TYR cc_start: 0.8451 (t80) cc_final: 0.8060 (t80) REVERT: C 2939 TYR cc_start: 0.8013 (m-80) cc_final: 0.7405 (m-80) REVERT: C 2943 PHE cc_start: 0.7833 (m-80) cc_final: 0.7351 (m-10) REVERT: C 2956 TYR cc_start: 0.8512 (m-80) cc_final: 0.8219 (m-10) REVERT: C 2980 LEU cc_start: 0.8967 (mm) cc_final: 0.8725 (mm) REVERT: C 3121 LEU cc_start: 0.8825 (tp) cc_final: 0.8513 (mt) REVERT: C 3131 TYR cc_start: 0.8759 (m-10) cc_final: 0.8429 (m-80) REVERT: C 3235 MET cc_start: 0.7348 (mtt) cc_final: 0.6805 (mtp) REVERT: C 3242 LEU cc_start: 0.9250 (mt) cc_final: 0.8794 (pp) REVERT: C 3245 TYR cc_start: 0.8507 (t80) cc_final: 0.8189 (t80) REVERT: C 4256 MET cc_start: 0.8314 (mtp) cc_final: 0.8099 (mtp) REVERT: C 4568 MET cc_start: 0.7440 (mmt) cc_final: 0.7178 (mmm) REVERT: C 4804 MET cc_start: 0.8984 (mmm) cc_final: 0.8776 (mmm) REVERT: J 13 PHE cc_start: 0.8946 (m-80) cc_final: 0.8611 (m-80) REVERT: J 64 ILE cc_start: 0.8341 (mm) cc_final: 0.8034 (tt) REVERT: J 69 PHE cc_start: 0.8281 (t80) cc_final: 0.8045 (t80) REVERT: J 145 MET cc_start: 0.1009 (pmm) cc_final: 0.0514 (pmm) REVERT: J 146 MET cc_start: -0.1460 (ptt) cc_final: -0.1977 (pp-130) REVERT: K 73 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7869 (pp-130) REVERT: K 145 MET cc_start: 0.1585 (pmm) cc_final: 0.1171 (pmm) REVERT: K 146 MET cc_start: 0.0370 (ptt) cc_final: -0.0361 (ppp) REVERT: L 1 MET cc_start: 0.6863 (mmt) cc_final: 0.6360 (mmp) REVERT: L 146 MET cc_start: 0.0619 (OUTLIER) cc_final: 0.0159 (pp-130) outliers start: 178 outliers final: 60 residues processed: 1196 average time/residue: 2.0836 time to fit residues: 3635.9311 Evaluate side-chains 1168 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1084 time to evaluate : 12.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 915 HIS Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2827 ASP Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 3033 LEU Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 1501 ASN Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2702 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 931 TYR Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2577 CYS Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 3003 MET Chi-restraints excluded: chain C residue 3034 HIS Chi-restraints excluded: chain C residue 3123 LEU Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1436 optimal weight: 0.6980 chunk 978 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 1283 optimal weight: 0.9990 chunk 711 optimal weight: 5.9990 chunk 1471 optimal weight: 2.9990 chunk 1191 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 880 optimal weight: 2.9990 chunk 1547 optimal weight: 20.0000 chunk 435 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2224 ASN A2684 ASN A2802 ASN ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 ASN A3127 GLN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 914 GLN D 915 HIS ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2684 ASN D2867 ASN D3095 ASN D3256 ASN B 395 HIS B 669 GLN ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN B3230 GLN B3252 HIS C 225 GLN C 669 GLN C 747 HIS C1562 ASN C2224 ASN C3034 HIS C3115 HIS ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 146296 Z= 0.191 Angle : 0.597 16.336 197604 Z= 0.300 Chirality : 0.040 0.348 21684 Planarity : 0.004 0.074 25424 Dihedral : 5.513 81.668 19654 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 1.01 % Allowed : 9.53 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.83 (0.06), residues: 17776 helix: 1.48 (0.06), residues: 9088 sheet: -0.18 (0.12), residues: 1676 loop : -0.43 (0.07), residues: 7012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A3295 HIS 0.019 0.001 HIS C3034 PHE 0.036 0.001 PHE C1979 TYR 0.037 0.001 TYR C1703 ARG 0.014 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1073 time to evaluate : 12.383 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 198 ASN cc_start: 0.7472 (p0) cc_final: 0.7197 (p0) REVERT: A 317 MET cc_start: 0.7620 (ptt) cc_final: 0.7414 (ptt) REVERT: A 393 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.6045 (mmm) REVERT: A 545 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7573 (tpp80) REVERT: A 892 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 938 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: A 1494 MET cc_start: 0.8354 (ppp) cc_final: 0.8134 (ppp) REVERT: A 1948 MET cc_start: 0.7236 (mmp) cc_final: 0.6906 (mmt) REVERT: A 1975 MET cc_start: 0.8262 (ptp) cc_final: 0.8032 (ptp) REVERT: A 2066 MET cc_start: 0.8897 (mmp) cc_final: 0.8617 (mmt) REVERT: A 2585 MET cc_start: 0.7918 (pmm) cc_final: 0.7596 (pmm) REVERT: A 2662 PHE cc_start: 0.8622 (m-10) cc_final: 0.8212 (m-80) REVERT: A 2688 MET cc_start: 0.3479 (OUTLIER) cc_final: 0.2921 (pp-130) REVERT: A 2719 TYR cc_start: 0.8342 (t80) cc_final: 0.7948 (t80) REVERT: A 2724 TYR cc_start: 0.8881 (t80) cc_final: 0.8242 (t80) REVERT: A 2850 ASN cc_start: 0.9234 (m-40) cc_final: 0.8504 (t0) REVERT: A 2867 ASN cc_start: 0.1562 (OUTLIER) cc_final: 0.1359 (p0) REVERT: A 3046 MET cc_start: 0.8295 (mpp) cc_final: 0.7456 (mpp) REVERT: A 3075 LEU cc_start: 0.8686 (pt) cc_final: 0.7928 (tt) REVERT: A 3123 LEU cc_start: 0.8978 (mt) cc_final: 0.8667 (mm) REVERT: A 3131 TYR cc_start: 0.8428 (m-10) cc_final: 0.8089 (m-80) REVERT: A 3159 LEU cc_start: 0.8808 (mt) cc_final: 0.8404 (mp) REVERT: A 3298 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8331 (mtm110) REVERT: A 3605 MET cc_start: 0.2986 (tmm) cc_final: 0.2214 (tpp) REVERT: A 4035 TYR cc_start: 0.7823 (m-80) cc_final: 0.7517 (m-80) REVERT: A 4268 MET cc_start: 0.5632 (mmm) cc_final: 0.5343 (tpt) REVERT: A 4707 MET cc_start: 0.8276 (ttp) cc_final: 0.7920 (ttm) REVERT: F 26 HIS cc_start: 0.9237 (OUTLIER) cc_final: 0.8731 (t-90) REVERT: F 58 LYS cc_start: 0.8315 (mtmp) cc_final: 0.8023 (ttpp) REVERT: I 77 MET cc_start: 0.8961 (tmm) cc_final: 0.8610 (tmm) REVERT: I 142 PHE cc_start: 0.6865 (t80) cc_final: 0.6648 (t80) REVERT: I 146 MET cc_start: 0.0313 (ptt) cc_final: -0.0256 (pmm) REVERT: D 42 PHE cc_start: 0.8404 (t80) cc_final: 0.8169 (t80) REVERT: D 317 MET cc_start: 0.7628 (ptt) cc_final: 0.7351 (ptt) REVERT: D 393 MET cc_start: 0.6663 (mmm) cc_final: 0.6110 (mmm) REVERT: D 399 MET cc_start: 0.7832 (pmm) cc_final: 0.7393 (tmm) REVERT: D 885 LEU cc_start: 0.9568 (mt) cc_final: 0.9337 (mm) REVERT: D 931 TYR cc_start: 0.7585 (t80) cc_final: 0.7313 (t80) REVERT: D 935 MET cc_start: 0.8369 (ptm) cc_final: 0.7957 (ptm) REVERT: D 940 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9131 (pt) REVERT: D 1062 TYR cc_start: 0.4685 (OUTLIER) cc_final: 0.2822 (m-80) REVERT: D 1165 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: D 1300 MET cc_start: 0.8556 (mmm) cc_final: 0.8260 (mmp) REVERT: D 1494 MET cc_start: 0.8451 (ppp) cc_final: 0.8175 (ppp) REVERT: D 1975 MET cc_start: 0.8189 (ptp) cc_final: 0.7969 (ptp) REVERT: D 2279 MET cc_start: 0.7972 (ptm) cc_final: 0.7739 (ttp) REVERT: D 2468 MET cc_start: 0.8717 (mmt) cc_final: 0.8459 (mmt) REVERT: D 2605 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: D 2662 PHE cc_start: 0.8816 (m-80) cc_final: 0.8368 (m-80) REVERT: D 2666 LEU cc_start: 0.9173 (tt) cc_final: 0.8904 (pp) REVERT: D 2688 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.4187 (pmt) REVERT: D 2704 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: D 2719 TYR cc_start: 0.8409 (t80) cc_final: 0.8000 (t80) REVERT: D 2724 TYR cc_start: 0.8954 (t80) cc_final: 0.8546 (t80) REVERT: D 2828 MET cc_start: 0.7367 (tpp) cc_final: 0.6671 (mmt) REVERT: D 2870 LEU cc_start: 0.8922 (mt) cc_final: 0.8658 (mm) REVERT: D 2895 PHE cc_start: 0.9174 (t80) cc_final: 0.8585 (t80) REVERT: D 3095 ASN cc_start: 0.8440 (m110) cc_final: 0.8180 (m-40) REVERT: D 3115 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7512 (m90) REVERT: D 3131 TYR cc_start: 0.8411 (m-10) cc_final: 0.8182 (m-80) REVERT: D 3211 LEU cc_start: 0.9001 (tp) cc_final: 0.8668 (pt) REVERT: D 3233 HIS cc_start: 0.8244 (t-90) cc_final: 0.7946 (t-90) REVERT: D 3235 MET cc_start: 0.7461 (mtm) cc_final: 0.6596 (tpt) REVERT: D 3323 MET cc_start: 0.7149 (mmm) cc_final: 0.6949 (mpm) REVERT: B 309 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6534 (mmm) REVERT: B 1975 MET cc_start: 0.8395 (ptp) cc_final: 0.7947 (ptp) REVERT: B 2347 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: B 2681 MET cc_start: 0.7698 (tpp) cc_final: 0.7437 (tpt) REVERT: B 2721 ILE cc_start: 0.9560 (mt) cc_final: 0.9277 (mm) REVERT: B 2724 TYR cc_start: 0.8995 (t80) cc_final: 0.8478 (t80) REVERT: B 2734 MET cc_start: 0.8211 (mpt) cc_final: 0.7885 (mpt) REVERT: B 2798 MET cc_start: 0.8867 (mmm) cc_final: 0.8379 (ptp) REVERT: B 2828 MET cc_start: 0.7560 (tpt) cc_final: 0.7051 (mmt) REVERT: B 2844 MET cc_start: 0.9009 (ppp) cc_final: 0.8705 (ppp) REVERT: B 2867 ASN cc_start: -0.0212 (OUTLIER) cc_final: -0.0549 (p0) REVERT: B 2880 LYS cc_start: 0.8916 (mppt) cc_final: 0.8565 (mppt) REVERT: B 2884 LYS cc_start: 0.8955 (mppt) cc_final: 0.8582 (tmtp) REVERT: B 2895 PHE cc_start: 0.9219 (t80) cc_final: 0.8728 (t80) REVERT: B 2939 TYR cc_start: 0.7907 (m-80) cc_final: 0.7410 (m-80) REVERT: B 2941 LEU cc_start: 0.9062 (pp) cc_final: 0.8614 (mt) REVERT: B 3046 MET cc_start: 0.8314 (mmm) cc_final: 0.7944 (mmm) REVERT: B 3214 LEU cc_start: 0.9232 (mp) cc_final: 0.8986 (mt) REVERT: B 3221 LEU cc_start: 0.8959 (pt) cc_final: 0.8720 (tp) REVERT: B 3233 HIS cc_start: 0.8195 (t-90) cc_final: 0.7980 (t-90) REVERT: B 3235 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6944 (mtt) REVERT: B 3242 LEU cc_start: 0.9351 (mt) cc_final: 0.8992 (pp) REVERT: B 3243 CYS cc_start: 0.8832 (m) cc_final: 0.8021 (m) REVERT: B 3250 TRP cc_start: 0.9396 (t60) cc_final: 0.9170 (t60) REVERT: B 3295 TRP cc_start: 0.8953 (p-90) cc_final: 0.8604 (p-90) REVERT: B 3299 LEU cc_start: 0.8941 (mt) cc_final: 0.8679 (mp) REVERT: B 3689 MET cc_start: 0.8415 (tpp) cc_final: 0.8168 (mtt) REVERT: B 3854 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8195 (t80) REVERT: C 895 MET cc_start: 0.7240 (mmt) cc_final: 0.6897 (mmm) REVERT: C 935 MET cc_start: 0.8782 (tmm) cc_final: 0.8367 (tmm) REVERT: C 999 LEU cc_start: 0.9514 (tm) cc_final: 0.9301 (pp) REVERT: C 1035 TYR cc_start: 0.8681 (t80) cc_final: 0.8462 (t80) REVERT: C 1165 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: C 1948 MET cc_start: 0.7207 (mmp) cc_final: 0.6798 (mmt) REVERT: C 2347 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: C 2585 MET cc_start: 0.8141 (ppp) cc_final: 0.7839 (pmm) REVERT: C 2731 LYS cc_start: 0.9336 (ptpp) cc_final: 0.9072 (pttm) REVERT: C 2737 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8600 (pp) REVERT: C 2798 MET cc_start: 0.8408 (mmm) cc_final: 0.7494 (ptm) REVERT: C 2848 TYR cc_start: 0.8635 (t80) cc_final: 0.8349 (t80) REVERT: C 2850 ASN cc_start: 0.9137 (m-40) cc_final: 0.8515 (t0) REVERT: C 2884 LYS cc_start: 0.9329 (mmpt) cc_final: 0.8872 (tmtt) REVERT: C 2923 TYR cc_start: 0.8361 (t80) cc_final: 0.7950 (t80) REVERT: C 2939 TYR cc_start: 0.8007 (m-80) cc_final: 0.7377 (m-80) REVERT: C 2943 PHE cc_start: 0.7841 (m-10) cc_final: 0.7357 (m-10) REVERT: C 2956 TYR cc_start: 0.8483 (m-80) cc_final: 0.8274 (m-10) REVERT: C 2980 LEU cc_start: 0.8920 (mm) cc_final: 0.8667 (mm) REVERT: C 3095 ASN cc_start: 0.7942 (m110) cc_final: 0.7719 (p0) REVERT: C 3121 LEU cc_start: 0.8792 (tp) cc_final: 0.8473 (mt) REVERT: C 3131 TYR cc_start: 0.8743 (m-10) cc_final: 0.8362 (m-80) REVERT: C 3223 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: C 3235 MET cc_start: 0.7174 (mtt) cc_final: 0.6531 (mpp) REVERT: C 3242 LEU cc_start: 0.9209 (mt) cc_final: 0.8753 (pp) REVERT: C 3245 TYR cc_start: 0.8334 (t80) cc_final: 0.8037 (t80) REVERT: C 4568 MET cc_start: 0.7450 (mmt) cc_final: 0.7205 (mmm) REVERT: J 13 PHE cc_start: 0.8953 (m-80) cc_final: 0.8584 (m-80) REVERT: J 64 ILE cc_start: 0.8310 (mm) cc_final: 0.8027 (tt) REVERT: J 145 MET cc_start: 0.0997 (pmm) cc_final: 0.0486 (pmm) REVERT: J 146 MET cc_start: -0.1464 (ptt) cc_final: -0.1970 (pp-130) REVERT: K 1 MET cc_start: 0.7014 (mmm) cc_final: 0.6585 (mmm) REVERT: K 73 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7942 (pp-130) REVERT: K 125 MET cc_start: 0.7154 (mpt) cc_final: 0.6935 (mpp) REVERT: K 145 MET cc_start: 0.1673 (pmm) cc_final: 0.1167 (pmm) REVERT: K 146 MET cc_start: 0.0277 (ptt) cc_final: -0.0420 (ppp) REVERT: L 52 MET cc_start: 0.8620 (ptt) cc_final: 0.8378 (ptt) REVERT: L 72 MET cc_start: 0.7704 (tpt) cc_final: 0.7455 (tpt) REVERT: L 145 MET cc_start: 0.3268 (pmm) cc_final: 0.2838 (pmt) REVERT: L 146 MET cc_start: 0.0422 (OUTLIER) cc_final: -0.0183 (pp-130) outliers start: 150 outliers final: 48 residues processed: 1149 average time/residue: 2.0072 time to fit residues: 3379.5927 Evaluate side-chains 1118 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1045 time to evaluate : 12.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2867 ASN Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3115 HIS Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3235 MET Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain D residue 915 HIS Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2688 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2704 GLN Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2737 LEU Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3034 HIS Chi-restraints excluded: chain C residue 3123 LEU Chi-restraints excluded: chain C residue 3223 GLU Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 580 optimal weight: 8.9990 chunk 1552 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 chunk 1012 optimal weight: 0.9980 chunk 425 optimal weight: 9.9990 chunk 1726 optimal weight: 6.9990 chunk 1432 optimal weight: 10.0000 chunk 799 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 570 optimal weight: 0.8980 chunk 906 optimal weight: 9.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2802 ASN D2867 ASN B 747 HIS ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN C 225 GLN C2867 ASN C3034 HIS ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 146296 Z= 0.338 Angle : 0.631 19.560 197604 Z= 0.317 Chirality : 0.042 0.404 21684 Planarity : 0.004 0.075 25424 Dihedral : 5.463 84.678 19652 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 1.00 % Allowed : 9.83 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.06), residues: 17776 helix: 1.52 (0.06), residues: 9104 sheet: -0.19 (0.12), residues: 1684 loop : -0.41 (0.07), residues: 6988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A3295 HIS 0.023 0.001 HIS C3034 PHE 0.044 0.002 PHE A1979 TYR 0.046 0.002 TYR C1703 ARG 0.016 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1086 time to evaluate : 12.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.7585 (p0) cc_final: 0.7312 (p0) REVERT: A 393 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6086 (mmm) REVERT: A 545 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7584 (tpp80) REVERT: A 892 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 938 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: A 1494 MET cc_start: 0.8418 (ppp) cc_final: 0.8181 (ppp) REVERT: A 1948 MET cc_start: 0.7228 (mmp) cc_final: 0.6929 (mmt) REVERT: A 1975 MET cc_start: 0.8309 (ptp) cc_final: 0.8077 (ptp) REVERT: A 2585 MET cc_start: 0.7971 (pmm) cc_final: 0.7707 (pmm) REVERT: A 2594 PHE cc_start: 0.8027 (m-80) cc_final: 0.7806 (m-80) REVERT: A 2662 PHE cc_start: 0.8738 (m-10) cc_final: 0.8325 (m-80) REVERT: A 2688 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.2868 (pp-130) REVERT: A 2719 TYR cc_start: 0.8427 (t80) cc_final: 0.8019 (t80) REVERT: A 2724 TYR cc_start: 0.8955 (t80) cc_final: 0.8688 (t80) REVERT: A 2729 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7774 (t-90) REVERT: A 2734 MET cc_start: 0.8051 (mmm) cc_final: 0.7611 (mpt) REVERT: A 2850 ASN cc_start: 0.9228 (m-40) cc_final: 0.8473 (t0) REVERT: A 3046 MET cc_start: 0.8277 (mpp) cc_final: 0.7474 (mpp) REVERT: A 3123 LEU cc_start: 0.9042 (mt) cc_final: 0.8741 (mm) REVERT: A 3131 TYR cc_start: 0.8491 (m-10) cc_final: 0.8169 (m-80) REVERT: A 3159 LEU cc_start: 0.8859 (mt) cc_final: 0.8437 (mp) REVERT: A 3605 MET cc_start: 0.2999 (tmm) cc_final: 0.2241 (tpt) REVERT: A 4035 TYR cc_start: 0.7889 (m-80) cc_final: 0.7574 (m-80) REVERT: A 4268 MET cc_start: 0.5678 (mmm) cc_final: 0.5404 (tpt) REVERT: A 4707 MET cc_start: 0.8284 (ttp) cc_final: 0.7916 (ttm) REVERT: F 26 HIS cc_start: 0.9272 (OUTLIER) cc_final: 0.8746 (t-90) REVERT: F 58 LYS cc_start: 0.8381 (mtmp) cc_final: 0.8122 (ttpp) REVERT: I 77 MET cc_start: 0.8903 (tmm) cc_final: 0.8591 (tmm) REVERT: I 146 MET cc_start: 0.0389 (ptt) cc_final: -0.0308 (pmm) REVERT: D 42 PHE cc_start: 0.8411 (t80) cc_final: 0.8167 (t80) REVERT: D 198 ASN cc_start: 0.7861 (p0) cc_final: 0.7551 (p0) REVERT: D 317 MET cc_start: 0.7655 (ptt) cc_final: 0.7365 (ptt) REVERT: D 399 MET cc_start: 0.7841 (pmm) cc_final: 0.7391 (tmm) REVERT: D 885 LEU cc_start: 0.9574 (mt) cc_final: 0.9348 (mm) REVERT: D 935 MET cc_start: 0.8399 (ptm) cc_final: 0.8019 (ptm) REVERT: D 940 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9151 (pt) REVERT: D 995 MET cc_start: 0.8258 (tmm) cc_final: 0.8020 (tpt) REVERT: D 1062 TYR cc_start: 0.4698 (OUTLIER) cc_final: 0.2858 (m-80) REVERT: D 1165 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8079 (mtp) REVERT: D 1300 MET cc_start: 0.8564 (mmm) cc_final: 0.8274 (mmp) REVERT: D 1494 MET cc_start: 0.8507 (ppp) cc_final: 0.8191 (ppp) REVERT: D 1975 MET cc_start: 0.8221 (ptp) cc_final: 0.8013 (ptp) REVERT: D 2150 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7720 (mtt) REVERT: D 2279 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: D 2590 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8285 (ttp80) REVERT: D 2605 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8487 (ttp) REVERT: D 2662 PHE cc_start: 0.8884 (m-80) cc_final: 0.8463 (m-80) REVERT: D 2666 LEU cc_start: 0.9239 (tt) cc_final: 0.8945 (pp) REVERT: D 2688 MET cc_start: 0.4591 (OUTLIER) cc_final: 0.4345 (pmt) REVERT: D 2719 TYR cc_start: 0.8454 (t80) cc_final: 0.8077 (t80) REVERT: D 2724 TYR cc_start: 0.8938 (t80) cc_final: 0.8407 (t80) REVERT: D 2734 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7360 (mtt) REVERT: D 2828 MET cc_start: 0.7437 (tpp) cc_final: 0.6752 (mmt) REVERT: D 2844 MET cc_start: 0.9048 (ppp) cc_final: 0.8764 (ppp) REVERT: D 2870 LEU cc_start: 0.8945 (mt) cc_final: 0.8686 (mm) REVERT: D 2880 LYS cc_start: 0.9063 (pmtt) cc_final: 0.8655 (ptmm) REVERT: D 2895 PHE cc_start: 0.9218 (t80) cc_final: 0.8604 (t80) REVERT: D 3046 MET cc_start: 0.7960 (mmm) cc_final: 0.7518 (mpm) REVERT: D 3095 ASN cc_start: 0.8541 (m110) cc_final: 0.8241 (m-40) REVERT: D 3131 TYR cc_start: 0.8443 (m-10) cc_final: 0.8193 (m-80) REVERT: D 3211 LEU cc_start: 0.9034 (tp) cc_final: 0.8731 (pt) REVERT: D 3233 HIS cc_start: 0.8247 (t-90) cc_final: 0.7975 (t-90) REVERT: B 309 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6535 (mmm) REVERT: B 1494 MET cc_start: 0.8895 (ppp) cc_final: 0.8671 (ppp) REVERT: B 1842 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 1948 MET cc_start: 0.7517 (mmp) cc_final: 0.7231 (mmt) REVERT: B 1975 MET cc_start: 0.8418 (ptp) cc_final: 0.8009 (ptp) REVERT: B 2347 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: B 2721 ILE cc_start: 0.9543 (mt) cc_final: 0.9334 (mm) REVERT: B 2724 TYR cc_start: 0.8999 (t80) cc_final: 0.8491 (t80) REVERT: B 2734 MET cc_start: 0.8249 (mpt) cc_final: 0.7867 (mpt) REVERT: B 2798 MET cc_start: 0.8870 (mmm) cc_final: 0.8307 (ptp) REVERT: B 2828 MET cc_start: 0.7585 (tpt) cc_final: 0.7018 (mmt) REVERT: B 2844 MET cc_start: 0.8995 (ppp) cc_final: 0.8675 (ppp) REVERT: B 2848 TYR cc_start: 0.8876 (t80) cc_final: 0.8584 (t80) REVERT: B 2867 ASN cc_start: -0.0208 (OUTLIER) cc_final: -0.0518 (p0) REVERT: B 2880 LYS cc_start: 0.8943 (mppt) cc_final: 0.8591 (mppt) REVERT: B 2884 LYS cc_start: 0.8965 (mppt) cc_final: 0.8570 (tmtp) REVERT: B 2895 PHE cc_start: 0.9233 (t80) cc_final: 0.8741 (t80) REVERT: B 2939 TYR cc_start: 0.7926 (m-80) cc_final: 0.7564 (m-80) REVERT: B 3046 MET cc_start: 0.8356 (mmm) cc_final: 0.7982 (mmm) REVERT: B 3214 LEU cc_start: 0.9215 (mp) cc_final: 0.8948 (mt) REVERT: B 3221 LEU cc_start: 0.8907 (pt) cc_final: 0.8694 (tp) REVERT: B 3233 HIS cc_start: 0.8287 (t-90) cc_final: 0.8079 (t-90) REVERT: B 3235 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6996 (mtt) REVERT: B 3242 LEU cc_start: 0.9360 (mt) cc_final: 0.9000 (pp) REVERT: B 3243 CYS cc_start: 0.8847 (m) cc_final: 0.8039 (m) REVERT: B 3250 TRP cc_start: 0.9397 (t60) cc_final: 0.9162 (t60) REVERT: B 3295 TRP cc_start: 0.8964 (p-90) cc_final: 0.8569 (p-90) REVERT: B 3299 LEU cc_start: 0.8959 (mt) cc_final: 0.8685 (mp) REVERT: B 3689 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (mtt) REVERT: B 3719 MET cc_start: 0.8032 (tpp) cc_final: 0.7831 (tpt) REVERT: B 3854 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8147 (t80) REVERT: C 225 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: C 935 MET cc_start: 0.8803 (tmm) cc_final: 0.8535 (ppp) REVERT: C 943 LEU cc_start: 0.8813 (mp) cc_final: 0.8416 (mm) REVERT: C 999 LEU cc_start: 0.9519 (tm) cc_final: 0.9225 (pp) REVERT: C 1035 TYR cc_start: 0.8720 (t80) cc_final: 0.8480 (t80) REVERT: C 1165 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: C 1948 MET cc_start: 0.7240 (mmp) cc_final: 0.6918 (mmt) REVERT: C 2347 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8183 (mtm) REVERT: C 2585 MET cc_start: 0.8168 (ppp) cc_final: 0.7909 (pmm) REVERT: C 2734 MET cc_start: 0.8456 (mmm) cc_final: 0.8231 (mpt) REVERT: C 2798 MET cc_start: 0.8335 (mmm) cc_final: 0.8133 (mmm) REVERT: C 2850 ASN cc_start: 0.9130 (m-40) cc_final: 0.8458 (t0) REVERT: C 2880 LYS cc_start: 0.9227 (mmtm) cc_final: 0.8983 (mppt) REVERT: C 2923 TYR cc_start: 0.8412 (t80) cc_final: 0.7995 (t80) REVERT: C 2939 TYR cc_start: 0.8062 (m-80) cc_final: 0.7449 (m-80) REVERT: C 2943 PHE cc_start: 0.7920 (m-10) cc_final: 0.7361 (m-10) REVERT: C 2980 LEU cc_start: 0.8967 (mm) cc_final: 0.8701 (mm) REVERT: C 3121 LEU cc_start: 0.8802 (tp) cc_final: 0.8502 (mt) REVERT: C 3131 TYR cc_start: 0.8760 (m-10) cc_final: 0.8439 (m-80) REVERT: C 3220 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8017 (tp30) REVERT: C 3235 MET cc_start: 0.7205 (mtt) cc_final: 0.6538 (mpp) REVERT: C 3242 LEU cc_start: 0.9209 (mt) cc_final: 0.8761 (pp) REVERT: C 3245 TYR cc_start: 0.8354 (t80) cc_final: 0.8095 (t80) REVERT: C 4568 MET cc_start: 0.7465 (mmt) cc_final: 0.7211 (mmm) REVERT: J 13 PHE cc_start: 0.9014 (m-80) cc_final: 0.8610 (m-80) REVERT: J 145 MET cc_start: 0.0961 (pmm) cc_final: 0.0513 (pmm) REVERT: J 146 MET cc_start: -0.1387 (ptt) cc_final: -0.1888 (pp-130) REVERT: K 64 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8064 (tt) REVERT: K 73 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7944 (pp-130) REVERT: K 125 MET cc_start: 0.7179 (mpt) cc_final: 0.6973 (mpp) REVERT: K 145 MET cc_start: 0.1614 (pmm) cc_final: 0.1126 (pmm) REVERT: K 146 MET cc_start: 0.0276 (ptt) cc_final: -0.0397 (ppp) REVERT: L 77 MET cc_start: 0.8826 (tmm) cc_final: 0.8612 (tpp) REVERT: L 146 MET cc_start: 0.0437 (OUTLIER) cc_final: -0.0100 (pp-130) outliers start: 149 outliers final: 67 residues processed: 1165 average time/residue: 2.0138 time to fit residues: 3428.0843 Evaluate side-chains 1162 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1067 time to evaluate : 12.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 915 HIS Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2729 HIS Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2983 LEU Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3115 HIS Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2688 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 1501 ASN Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1896 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3123 LEU Chi-restraints excluded: chain C residue 3184 TYR Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1664 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 983 optimal weight: 7.9990 chunk 1260 optimal weight: 4.9990 chunk 976 optimal weight: 4.9990 chunk 1453 optimal weight: 1.9990 chunk 963 optimal weight: 10.0000 chunk 1719 optimal weight: 7.9990 chunk 1076 optimal weight: 6.9990 chunk 1048 optimal weight: 4.9990 chunk 793 optimal weight: 0.0670 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C3115 HIS ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 146296 Z= 0.237 Angle : 0.611 17.891 197604 Z= 0.304 Chirality : 0.041 0.393 21684 Planarity : 0.004 0.085 25424 Dihedral : 5.341 85.893 19650 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 0.92 % Allowed : 10.17 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.95 (0.06), residues: 17776 helix: 1.59 (0.06), residues: 9088 sheet: -0.16 (0.12), residues: 1684 loop : -0.37 (0.08), residues: 7004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A3295 HIS 0.020 0.001 HIS A3034 PHE 0.043 0.001 PHE A1979 TYR 0.043 0.001 TYR C2719 ARG 0.016 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1076 time to evaluate : 12.424 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: A 198 ASN cc_start: 0.7561 (p0) cc_final: 0.7264 (p0) REVERT: A 393 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6161 (mmm) REVERT: A 545 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7554 (tpp80) REVERT: A 892 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8970 (mt) REVERT: A 938 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 940 LEU cc_start: 0.9456 (mp) cc_final: 0.9213 (pt) REVERT: A 1494 MET cc_start: 0.8372 (ppp) cc_final: 0.8159 (ppp) REVERT: A 1948 MET cc_start: 0.7220 (mmp) cc_final: 0.6837 (tpp) REVERT: A 1975 MET cc_start: 0.8312 (ptp) cc_final: 0.8057 (ptp) REVERT: A 2585 MET cc_start: 0.7965 (pmm) cc_final: 0.7622 (pmm) REVERT: A 2662 PHE cc_start: 0.8757 (m-10) cc_final: 0.8115 (m-80) REVERT: A 2666 LEU cc_start: 0.9321 (tp) cc_final: 0.9006 (pp) REVERT: A 2688 MET cc_start: 0.3506 (OUTLIER) cc_final: 0.2888 (pp-130) REVERT: A 2719 TYR cc_start: 0.8425 (t80) cc_final: 0.8016 (t80) REVERT: A 2724 TYR cc_start: 0.8941 (t80) cc_final: 0.8542 (t80) REVERT: A 2729 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (t-90) REVERT: A 2734 MET cc_start: 0.8116 (mmm) cc_final: 0.7720 (mpt) REVERT: A 2850 ASN cc_start: 0.9226 (m-40) cc_final: 0.8455 (t0) REVERT: A 2939 TYR cc_start: 0.8295 (m-80) cc_final: 0.7675 (m-80) REVERT: A 3046 MET cc_start: 0.8280 (mpp) cc_final: 0.7646 (mpt) REVERT: A 3123 LEU cc_start: 0.9015 (mt) cc_final: 0.8782 (mm) REVERT: A 3131 TYR cc_start: 0.8482 (m-10) cc_final: 0.8156 (m-80) REVERT: A 3159 LEU cc_start: 0.8876 (mt) cc_final: 0.8425 (mp) REVERT: A 3298 ARG cc_start: 0.8645 (ptm160) cc_final: 0.8263 (ptm160) REVERT: A 3605 MET cc_start: 0.3031 (tmm) cc_final: 0.2272 (tpt) REVERT: A 4268 MET cc_start: 0.5685 (mmm) cc_final: 0.5414 (tpt) REVERT: A 4707 MET cc_start: 0.8273 (ttp) cc_final: 0.7920 (ttm) REVERT: F 26 HIS cc_start: 0.9247 (OUTLIER) cc_final: 0.8786 (t-90) REVERT: F 58 LYS cc_start: 0.8376 (mtmp) cc_final: 0.8091 (ttpp) REVERT: I 73 MET cc_start: 0.8494 (ttp) cc_final: 0.8090 (tmm) REVERT: I 77 MET cc_start: 0.8987 (tmm) cc_final: 0.8493 (tmm) REVERT: I 125 MET cc_start: 0.7574 (mpt) cc_final: 0.7262 (mpm) REVERT: I 142 PHE cc_start: 0.6886 (t80) cc_final: 0.6638 (t80) REVERT: I 146 MET cc_start: 0.0443 (ptt) cc_final: -0.0232 (pmm) REVERT: D 42 PHE cc_start: 0.8395 (t80) cc_final: 0.8163 (t80) REVERT: D 241 MET cc_start: 0.6367 (mmt) cc_final: 0.6008 (mmp) REVERT: D 317 MET cc_start: 0.7634 (ptt) cc_final: 0.7358 (ptt) REVERT: D 399 MET cc_start: 0.7837 (pmm) cc_final: 0.7398 (tmm) REVERT: D 885 LEU cc_start: 0.9573 (mt) cc_final: 0.9345 (mm) REVERT: D 935 MET cc_start: 0.8370 (ptm) cc_final: 0.7977 (ptm) REVERT: D 995 MET cc_start: 0.8252 (tmm) cc_final: 0.8023 (tpt) REVERT: D 1062 TYR cc_start: 0.4551 (OUTLIER) cc_final: 0.2775 (m-80) REVERT: D 1165 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: D 1300 MET cc_start: 0.8551 (mmm) cc_final: 0.8257 (mmp) REVERT: D 1494 MET cc_start: 0.8534 (ppp) cc_final: 0.8204 (ppp) REVERT: D 2150 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: D 2279 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: D 2468 MET cc_start: 0.8750 (mmt) cc_final: 0.8399 (mmt) REVERT: D 2590 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8073 (ttp80) REVERT: D 2605 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8479 (ttp) REVERT: D 2662 PHE cc_start: 0.8873 (m-80) cc_final: 0.8427 (m-80) REVERT: D 2666 LEU cc_start: 0.9243 (tt) cc_final: 0.8954 (pp) REVERT: D 2695 MET cc_start: 0.8158 (mpt) cc_final: 0.7064 (mmt) REVERT: D 2719 TYR cc_start: 0.8452 (t80) cc_final: 0.8028 (t80) REVERT: D 2734 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7365 (mtt) REVERT: D 2828 MET cc_start: 0.7375 (tpp) cc_final: 0.6711 (mmt) REVERT: D 2870 LEU cc_start: 0.8941 (mt) cc_final: 0.8687 (mm) REVERT: D 2880 LYS cc_start: 0.9076 (pmtt) cc_final: 0.8668 (ptmm) REVERT: D 2895 PHE cc_start: 0.9200 (t80) cc_final: 0.8628 (t80) REVERT: D 2983 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mm) REVERT: D 3046 MET cc_start: 0.7961 (mmm) cc_final: 0.7488 (mpm) REVERT: D 3095 ASN cc_start: 0.8544 (m110) cc_final: 0.8238 (m-40) REVERT: D 3131 TYR cc_start: 0.8430 (m-10) cc_final: 0.8183 (m-80) REVERT: D 3211 LEU cc_start: 0.8994 (tp) cc_final: 0.8705 (pt) REVERT: D 3233 HIS cc_start: 0.8267 (t-90) cc_final: 0.7984 (t-90) REVERT: D 3235 MET cc_start: 0.7711 (mtm) cc_final: 0.6678 (pmm) REVERT: D 3323 MET cc_start: 0.7189 (mmm) cc_final: 0.6989 (mpm) REVERT: D 3954 MET cc_start: 0.8254 (mtp) cc_final: 0.8031 (mtt) REVERT: B 309 MET cc_start: 0.6784 (mpm) cc_final: 0.6546 (mmm) REVERT: B 1948 MET cc_start: 0.7520 (mmp) cc_final: 0.7245 (mmt) REVERT: B 1975 MET cc_start: 0.8416 (ptp) cc_final: 0.7978 (ptp) REVERT: B 2347 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8484 (mtm) REVERT: B 2681 MET cc_start: 0.7718 (tpp) cc_final: 0.7414 (tpt) REVERT: B 2724 TYR cc_start: 0.8994 (t80) cc_final: 0.8496 (t80) REVERT: B 2798 MET cc_start: 0.8875 (mmm) cc_final: 0.8353 (ptp) REVERT: B 2828 MET cc_start: 0.7626 (tpt) cc_final: 0.7027 (mmt) REVERT: B 2833 LEU cc_start: 0.8533 (mp) cc_final: 0.8294 (mp) REVERT: B 2848 TYR cc_start: 0.8878 (t80) cc_final: 0.8617 (t80) REVERT: B 2867 ASN cc_start: -0.0439 (OUTLIER) cc_final: -0.0703 (p0) REVERT: B 2880 LYS cc_start: 0.8958 (mppt) cc_final: 0.8592 (mppt) REVERT: B 2884 LYS cc_start: 0.8912 (mppt) cc_final: 0.8525 (tmtp) REVERT: B 2895 PHE cc_start: 0.9222 (t80) cc_final: 0.8697 (t80) REVERT: B 2939 TYR cc_start: 0.7909 (m-80) cc_final: 0.7540 (m-80) REVERT: B 3046 MET cc_start: 0.8347 (mmm) cc_final: 0.7969 (mmm) REVERT: B 3115 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8747 (m90) REVERT: B 3214 LEU cc_start: 0.9207 (mp) cc_final: 0.8945 (mt) REVERT: B 3235 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: B 3242 LEU cc_start: 0.9328 (mt) cc_final: 0.8985 (pp) REVERT: B 3243 CYS cc_start: 0.8840 (m) cc_final: 0.8025 (m) REVERT: B 3250 TRP cc_start: 0.9382 (t60) cc_final: 0.9146 (t60) REVERT: B 3295 TRP cc_start: 0.8949 (p-90) cc_final: 0.8564 (p-90) REVERT: B 3299 LEU cc_start: 0.8958 (mt) cc_final: 0.8695 (mp) REVERT: B 3689 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8199 (mtt) REVERT: B 3854 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8245 (t80) REVERT: B 3981 MET cc_start: 0.8661 (tmm) cc_final: 0.8371 (ttp) REVERT: C 895 MET cc_start: 0.7377 (mmt) cc_final: 0.6987 (mmt) REVERT: C 935 MET cc_start: 0.8796 (tmm) cc_final: 0.8491 (ppp) REVERT: C 995 MET cc_start: 0.8400 (tmm) cc_final: 0.8193 (tmm) REVERT: C 1035 TYR cc_start: 0.8703 (t80) cc_final: 0.8465 (t80) REVERT: C 1165 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: C 1948 MET cc_start: 0.7217 (mmp) cc_final: 0.6912 (mmt) REVERT: C 2347 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8153 (mtm) REVERT: C 2585 MET cc_start: 0.8212 (ppp) cc_final: 0.7873 (pmm) REVERT: C 2666 LEU cc_start: 0.9245 (tt) cc_final: 0.8861 (pt) REVERT: C 2734 MET cc_start: 0.8447 (mmm) cc_final: 0.8232 (mpt) REVERT: C 2798 MET cc_start: 0.8381 (mmm) cc_final: 0.7539 (ptm) REVERT: C 2828 MET cc_start: 0.7065 (tpt) cc_final: 0.6860 (tpt) REVERT: C 2850 ASN cc_start: 0.9134 (m-40) cc_final: 0.8516 (t0) REVERT: C 2880 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8988 (mppt) REVERT: C 2884 LYS cc_start: 0.9356 (mmpt) cc_final: 0.8921 (tmtt) REVERT: C 2885 ASP cc_start: 0.8794 (m-30) cc_final: 0.8442 (m-30) REVERT: C 2923 TYR cc_start: 0.8368 (t80) cc_final: 0.7963 (t80) REVERT: C 2939 TYR cc_start: 0.8069 (m-80) cc_final: 0.7505 (m-80) REVERT: C 2943 PHE cc_start: 0.7912 (m-10) cc_final: 0.7461 (m-10) REVERT: C 2980 LEU cc_start: 0.8951 (mm) cc_final: 0.8685 (mm) REVERT: C 3104 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7861 (tpt) REVERT: C 3121 LEU cc_start: 0.8771 (tp) cc_final: 0.8479 (mt) REVERT: C 3131 TYR cc_start: 0.8774 (m-10) cc_final: 0.8398 (m-80) REVERT: C 3220 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8068 (tp30) REVERT: C 3235 MET cc_start: 0.7053 (mtt) cc_final: 0.6392 (mpp) REVERT: C 3242 LEU cc_start: 0.9211 (mt) cc_final: 0.8684 (pp) REVERT: C 3245 TYR cc_start: 0.8359 (t80) cc_final: 0.8130 (t80) REVERT: C 3252 HIS cc_start: 0.7998 (m90) cc_final: 0.7712 (m-70) REVERT: C 4568 MET cc_start: 0.7473 (mmt) cc_final: 0.7221 (mmm) REVERT: C 4707 MET cc_start: 0.8357 (ttm) cc_final: 0.8150 (ttm) REVERT: J 145 MET cc_start: 0.1013 (pmm) cc_final: 0.0395 (ppp) REVERT: J 146 MET cc_start: -0.1364 (ptt) cc_final: -0.1800 (pp-130) REVERT: K 73 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (ppp) REVERT: K 145 MET cc_start: 0.1597 (pmm) cc_final: 0.1123 (pmm) REVERT: K 146 MET cc_start: 0.0160 (ptt) cc_final: -0.0478 (ppp) REVERT: L 9 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: L 37 MET cc_start: 0.9298 (mpt) cc_final: 0.8955 (pmm) REVERT: L 77 MET cc_start: 0.8895 (tmm) cc_final: 0.8580 (tpp) REVERT: L 145 MET cc_start: 0.2952 (pmm) cc_final: 0.2599 (pmt) REVERT: L 146 MET cc_start: 0.0531 (OUTLIER) cc_final: -0.0065 (pp-130) outliers start: 137 outliers final: 58 residues processed: 1147 average time/residue: 2.0527 time to fit residues: 3432.6023 Evaluate side-chains 1142 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1058 time to evaluate : 12.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2729 HIS Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2890 GLN Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3829 VAL Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1501 ASN Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2720 PHE Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1063 optimal weight: 0.9990 chunk 686 optimal weight: 8.9990 chunk 1026 optimal weight: 1.9990 chunk 517 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 333 optimal weight: 0.9980 chunk 1093 optimal weight: 5.9990 chunk 1171 optimal weight: 20.0000 chunk 850 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 1351 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C3095 ASN C3115 HIS ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 146296 Z= 0.206 Angle : 0.613 19.176 197604 Z= 0.303 Chirality : 0.040 0.387 21684 Planarity : 0.004 0.090 25424 Dihedral : 5.246 86.722 19650 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 0.84 % Allowed : 10.39 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.06), residues: 17776 helix: 1.64 (0.06), residues: 9096 sheet: -0.13 (0.12), residues: 1704 loop : -0.34 (0.08), residues: 6976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP A3295 HIS 0.020 0.001 HIS A3034 PHE 0.077 0.001 PHE B2720 TYR 0.030 0.001 TYR A2939 ARG 0.018 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1076 time to evaluate : 12.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 26 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8246 (t-90) REVERT: A 198 ASN cc_start: 0.7565 (p0) cc_final: 0.7303 (p0) REVERT: A 393 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6178 (mmm) REVERT: A 545 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7558 (tpp80) REVERT: A 892 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8934 (mt) REVERT: A 938 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: A 940 LEU cc_start: 0.9452 (mp) cc_final: 0.9212 (pt) REVERT: A 1494 MET cc_start: 0.8382 (ppp) cc_final: 0.8173 (ppp) REVERT: A 1948 MET cc_start: 0.7220 (mmp) cc_final: 0.6835 (tpp) REVERT: A 1975 MET cc_start: 0.8312 (ptp) cc_final: 0.8061 (ptp) REVERT: A 2585 MET cc_start: 0.8073 (pmm) cc_final: 0.7756 (pmm) REVERT: A 2662 PHE cc_start: 0.8775 (m-10) cc_final: 0.8143 (m-80) REVERT: A 2666 LEU cc_start: 0.9318 (tp) cc_final: 0.9015 (pp) REVERT: A 2688 MET cc_start: 0.3439 (OUTLIER) cc_final: 0.2824 (pp-130) REVERT: A 2719 TYR cc_start: 0.8419 (t80) cc_final: 0.8008 (t80) REVERT: A 2729 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7760 (t-90) REVERT: A 2734 MET cc_start: 0.8146 (mmm) cc_final: 0.7739 (mpt) REVERT: A 2850 ASN cc_start: 0.9200 (m-40) cc_final: 0.8428 (t0) REVERT: A 2880 LYS cc_start: 0.8784 (mppt) cc_final: 0.8560 (mppt) REVERT: A 3046 MET cc_start: 0.8275 (mpp) cc_final: 0.7631 (mpt) REVERT: A 3072 MET cc_start: 0.8223 (mmt) cc_final: 0.7890 (mtt) REVERT: A 3123 LEU cc_start: 0.9033 (mt) cc_final: 0.8768 (mm) REVERT: A 3131 TYR cc_start: 0.8487 (m-10) cc_final: 0.8160 (m-80) REVERT: A 3159 LEU cc_start: 0.8867 (mt) cc_final: 0.8405 (mp) REVERT: A 3235 MET cc_start: 0.6857 (mmt) cc_final: 0.6629 (mmt) REVERT: A 3298 ARG cc_start: 0.8643 (ptm160) cc_final: 0.8243 (ptm160) REVERT: A 3323 MET cc_start: 0.7626 (mpm) cc_final: 0.7343 (mpm) REVERT: A 3605 MET cc_start: 0.2947 (tmm) cc_final: 0.2577 (tpp) REVERT: A 4707 MET cc_start: 0.8278 (ttp) cc_final: 0.7890 (ttm) REVERT: F 58 LYS cc_start: 0.8326 (mtmp) cc_final: 0.8066 (ttpp) REVERT: I 70 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8249 (mp) REVERT: I 73 MET cc_start: 0.8571 (ttp) cc_final: 0.8081 (tmm) REVERT: I 125 MET cc_start: 0.7592 (mpt) cc_final: 0.7274 (mpm) REVERT: I 142 PHE cc_start: 0.6894 (t80) cc_final: 0.6640 (t80) REVERT: I 146 MET cc_start: 0.0390 (ptt) cc_final: -0.0257 (pmm) REVERT: D 42 PHE cc_start: 0.8400 (t80) cc_final: 0.8169 (t80) REVERT: D 241 MET cc_start: 0.6350 (mmt) cc_final: 0.6123 (mpm) REVERT: D 317 MET cc_start: 0.7606 (ptt) cc_final: 0.7340 (ptt) REVERT: D 399 MET cc_start: 0.7843 (pmm) cc_final: 0.7403 (tmm) REVERT: D 885 LEU cc_start: 0.9579 (mt) cc_final: 0.9346 (mm) REVERT: D 935 MET cc_start: 0.8366 (ptm) cc_final: 0.7983 (ptm) REVERT: D 1062 TYR cc_start: 0.4439 (OUTLIER) cc_final: 0.2653 (m-80) REVERT: D 1165 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7986 (mtt) REVERT: D 1300 MET cc_start: 0.8544 (mmm) cc_final: 0.8246 (mmp) REVERT: D 1494 MET cc_start: 0.8561 (ppp) cc_final: 0.8238 (ppp) REVERT: D 1975 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7991 (ptp) REVERT: D 2150 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7667 (mtt) REVERT: D 2279 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7730 (ttp) REVERT: D 2468 MET cc_start: 0.8748 (mmt) cc_final: 0.8404 (mmt) REVERT: D 2590 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8324 (ttp80) REVERT: D 2605 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: D 2662 PHE cc_start: 0.8872 (m-80) cc_final: 0.8443 (m-80) REVERT: D 2666 LEU cc_start: 0.9249 (tt) cc_final: 0.8963 (pp) REVERT: D 2695 MET cc_start: 0.8167 (mpt) cc_final: 0.7192 (mmt) REVERT: D 2719 TYR cc_start: 0.8410 (t80) cc_final: 0.7975 (t80) REVERT: D 2734 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7361 (mtt) REVERT: D 2828 MET cc_start: 0.7374 (tpp) cc_final: 0.6735 (mmt) REVERT: D 2844 MET cc_start: 0.9039 (ppp) cc_final: 0.8706 (ppp) REVERT: D 2870 LEU cc_start: 0.8947 (mt) cc_final: 0.8699 (mm) REVERT: D 2880 LYS cc_start: 0.9078 (pmtt) cc_final: 0.8665 (ptmm) REVERT: D 2895 PHE cc_start: 0.9175 (t80) cc_final: 0.8610 (t80) REVERT: D 2983 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8500 (mm) REVERT: D 3046 MET cc_start: 0.7964 (mmm) cc_final: 0.7511 (mpm) REVERT: D 3095 ASN cc_start: 0.8557 (m110) cc_final: 0.8247 (m-40) REVERT: D 3131 TYR cc_start: 0.8399 (m-10) cc_final: 0.8147 (m-80) REVERT: D 3211 LEU cc_start: 0.8995 (tp) cc_final: 0.8600 (pt) REVERT: D 3233 HIS cc_start: 0.8181 (t-90) cc_final: 0.7924 (t-90) REVERT: D 3235 MET cc_start: 0.7626 (mtm) cc_final: 0.6548 (pmm) REVERT: D 3854 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8073 (t80) REVERT: D 3954 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: B 309 MET cc_start: 0.6841 (mpm) cc_final: 0.6585 (mmm) REVERT: B 981 MET cc_start: 0.5968 (tmm) cc_final: 0.5744 (tpp) REVERT: B 1948 MET cc_start: 0.7524 (mmp) cc_final: 0.7255 (mmt) REVERT: B 1975 MET cc_start: 0.8405 (ptp) cc_final: 0.7974 (ptp) REVERT: B 2347 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: B 2456 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (mmm) REVERT: B 2720 PHE cc_start: 0.9001 (t80) cc_final: 0.8692 (t80) REVERT: B 2724 TYR cc_start: 0.8888 (t80) cc_final: 0.8494 (t80) REVERT: B 2734 MET cc_start: 0.8232 (mpt) cc_final: 0.7679 (mpt) REVERT: B 2798 MET cc_start: 0.8858 (mmm) cc_final: 0.8284 (ptp) REVERT: B 2828 MET cc_start: 0.7581 (tpt) cc_final: 0.6978 (mmt) REVERT: B 2844 MET cc_start: 0.8865 (ppp) cc_final: 0.8547 (ppp) REVERT: B 2848 TYR cc_start: 0.8795 (t80) cc_final: 0.8519 (t80) REVERT: B 2867 ASN cc_start: -0.0813 (OUTLIER) cc_final: -0.1134 (p0) REVERT: B 2880 LYS cc_start: 0.8973 (mppt) cc_final: 0.8596 (mppt) REVERT: B 2884 LYS cc_start: 0.8908 (mppt) cc_final: 0.8530 (tmtp) REVERT: B 2895 PHE cc_start: 0.9246 (t80) cc_final: 0.8738 (t80) REVERT: B 2939 TYR cc_start: 0.7922 (m-80) cc_final: 0.7512 (m-80) REVERT: B 2941 LEU cc_start: 0.9013 (pt) cc_final: 0.8595 (mm) REVERT: B 3046 MET cc_start: 0.8340 (mmm) cc_final: 0.7994 (mmm) REVERT: B 3115 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8736 (m90) REVERT: B 3214 LEU cc_start: 0.9199 (mp) cc_final: 0.8935 (mt) REVERT: B 3233 HIS cc_start: 0.8226 (t-90) cc_final: 0.7949 (t-90) REVERT: B 3235 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: B 3242 LEU cc_start: 0.9324 (mt) cc_final: 0.8989 (pp) REVERT: B 3243 CYS cc_start: 0.8815 (m) cc_final: 0.7986 (m) REVERT: B 3250 TRP cc_start: 0.9367 (t60) cc_final: 0.9115 (t60) REVERT: B 3295 TRP cc_start: 0.8935 (p-90) cc_final: 0.8668 (p-90) REVERT: B 3689 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: B 3719 MET cc_start: 0.8058 (tpp) cc_final: 0.7800 (tpt) REVERT: B 3854 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8228 (t80) REVERT: B 3981 MET cc_start: 0.8676 (tmm) cc_final: 0.8360 (ttp) REVERT: C 895 MET cc_start: 0.7332 (mmt) cc_final: 0.6995 (mmm) REVERT: C 935 MET cc_start: 0.8812 (tmm) cc_final: 0.8505 (ppp) REVERT: C 1035 TYR cc_start: 0.8705 (t80) cc_final: 0.8476 (t80) REVERT: C 1165 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: C 1494 MET cc_start: 0.8678 (ppp) cc_final: 0.8477 (ppp) REVERT: C 1948 MET cc_start: 0.7179 (mmp) cc_final: 0.6882 (mmt) REVERT: C 2347 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8143 (mtm) REVERT: C 2585 MET cc_start: 0.8258 (ppp) cc_final: 0.7787 (pmm) REVERT: C 2666 LEU cc_start: 0.9255 (tt) cc_final: 0.8921 (pp) REVERT: C 2850 ASN cc_start: 0.9130 (m-40) cc_final: 0.8496 (t0) REVERT: C 2880 LYS cc_start: 0.9267 (mmtm) cc_final: 0.9043 (mppt) REVERT: C 2884 LYS cc_start: 0.9365 (mmpt) cc_final: 0.8901 (tmtt) REVERT: C 2923 TYR cc_start: 0.8361 (t80) cc_final: 0.7969 (t80) REVERT: C 2939 TYR cc_start: 0.8045 (m-80) cc_final: 0.7514 (m-80) REVERT: C 2943 PHE cc_start: 0.7915 (m-10) cc_final: 0.7439 (m-10) REVERT: C 2980 LEU cc_start: 0.8938 (mm) cc_final: 0.8675 (mm) REVERT: C 3095 ASN cc_start: 0.9011 (t0) cc_final: 0.8459 (m110) REVERT: C 3104 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7854 (tpt) REVERT: C 3121 LEU cc_start: 0.8768 (tp) cc_final: 0.8465 (mt) REVERT: C 3131 TYR cc_start: 0.8756 (m-10) cc_final: 0.8415 (m-80) REVERT: C 3223 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: C 3235 MET cc_start: 0.7039 (mtt) cc_final: 0.6397 (mpp) REVERT: C 3242 LEU cc_start: 0.9165 (mt) cc_final: 0.8701 (pp) REVERT: C 3245 TYR cc_start: 0.8390 (t80) cc_final: 0.8128 (t80) REVERT: C 3252 HIS cc_start: 0.7998 (m90) cc_final: 0.7689 (m-70) REVERT: C 4568 MET cc_start: 0.7474 (mmt) cc_final: 0.7221 (mmm) REVERT: C 4707 MET cc_start: 0.8379 (ttm) cc_final: 0.8141 (ttt) REVERT: J 1 MET cc_start: 0.6527 (mmm) cc_final: 0.6259 (tpp) REVERT: J 69 PHE cc_start: 0.8274 (t80) cc_final: 0.8029 (t80) REVERT: J 145 MET cc_start: 0.0998 (pmm) cc_final: 0.0359 (pp-130) REVERT: J 146 MET cc_start: -0.1281 (ptt) cc_final: -0.1877 (pp-130) REVERT: K 69 PHE cc_start: 0.8141 (t80) cc_final: 0.7874 (t80) REVERT: K 145 MET cc_start: 0.1575 (pmm) cc_final: 0.1027 (pmm) REVERT: K 146 MET cc_start: 0.0244 (ptt) cc_final: -0.0419 (ppp) REVERT: L 9 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: L 77 MET cc_start: 0.8829 (tmm) cc_final: 0.8604 (tpp) REVERT: L 145 MET cc_start: 0.2459 (pmm) cc_final: 0.2182 (pmt) REVERT: L 146 MET cc_start: 0.0524 (OUTLIER) cc_final: -0.0188 (pp-130) outliers start: 124 outliers final: 50 residues processed: 1139 average time/residue: 2.0133 time to fit residues: 3347.9589 Evaluate side-chains 1144 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1063 time to evaluate : 12.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2729 HIS Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3829 VAL Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 2347 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3223 GLU Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1564 optimal weight: 0.9990 chunk 1647 optimal weight: 7.9990 chunk 1502 optimal weight: 10.0000 chunk 1602 optimal weight: 8.9990 chunk 1646 optimal weight: 0.8980 chunk 964 optimal weight: 0.5980 chunk 698 optimal weight: 20.0000 chunk 1258 optimal weight: 5.9990 chunk 491 optimal weight: 6.9990 chunk 1447 optimal weight: 10.0000 chunk 1515 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN D3286 ASN B 395 HIS ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3127 GLN C3304 GLN ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 146296 Z= 0.221 Angle : 0.625 20.330 197604 Z= 0.307 Chirality : 0.041 0.428 21684 Planarity : 0.004 0.114 25424 Dihedral : 5.204 87.333 19650 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 0.76 % Allowed : 10.69 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.06), residues: 17776 helix: 1.67 (0.06), residues: 9064 sheet: -0.11 (0.12), residues: 1704 loop : -0.34 (0.08), residues: 7008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A3295 HIS 0.023 0.001 HIS A3034 PHE 0.049 0.001 PHE A1979 TYR 0.044 0.001 TYR C2719 ARG 0.018 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1071 time to evaluate : 12.536 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: H 67 MET cc_start: 0.8821 (ttm) cc_final: 0.8565 (mtp) REVERT: A 198 ASN cc_start: 0.7559 (p0) cc_final: 0.7295 (p0) REVERT: A 393 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6195 (mmm) REVERT: A 545 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7559 (tpp80) REVERT: A 892 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 938 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 940 LEU cc_start: 0.9454 (mp) cc_final: 0.9220 (pt) REVERT: A 1948 MET cc_start: 0.7221 (mmp) cc_final: 0.6981 (mmp) REVERT: A 1975 MET cc_start: 0.8305 (ptp) cc_final: 0.8051 (ptp) REVERT: A 2214 MET cc_start: 0.8895 (mmp) cc_final: 0.8642 (mmm) REVERT: A 2585 MET cc_start: 0.8081 (pmm) cc_final: 0.7774 (pmm) REVERT: A 2662 PHE cc_start: 0.8791 (m-10) cc_final: 0.8379 (m-80) REVERT: A 2688 MET cc_start: 0.3471 (OUTLIER) cc_final: 0.2910 (pp-130) REVERT: A 2719 TYR cc_start: 0.8404 (t80) cc_final: 0.8012 (t80) REVERT: A 2732 TRP cc_start: 0.8745 (t60) cc_final: 0.8523 (t60) REVERT: A 2734 MET cc_start: 0.8160 (mmm) cc_final: 0.7765 (mpt) REVERT: A 2844 MET cc_start: 0.8850 (ppp) cc_final: 0.8470 (ppp) REVERT: A 2850 ASN cc_start: 0.9198 (m-40) cc_final: 0.8418 (t0) REVERT: A 2880 LYS cc_start: 0.8792 (mppt) cc_final: 0.8544 (mppt) REVERT: A 3046 MET cc_start: 0.8309 (mpp) cc_final: 0.7509 (mpp) REVERT: A 3104 MET cc_start: 0.8200 (tmt) cc_final: 0.7996 (tmt) REVERT: A 3131 TYR cc_start: 0.8488 (m-10) cc_final: 0.8166 (m-80) REVERT: A 3159 LEU cc_start: 0.8862 (mt) cc_final: 0.8388 (mp) REVERT: A 3235 MET cc_start: 0.6827 (mmt) cc_final: 0.6595 (mmt) REVERT: A 3263 MET cc_start: 0.4906 (ppp) cc_final: 0.4443 (pmm) REVERT: A 3298 ARG cc_start: 0.8658 (ptm160) cc_final: 0.8252 (ptm160) REVERT: A 3323 MET cc_start: 0.7629 (mpm) cc_final: 0.7328 (mpm) REVERT: A 3605 MET cc_start: 0.2968 (tmm) cc_final: 0.2637 (tpp) REVERT: A 4035 TYR cc_start: 0.7789 (m-80) cc_final: 0.7437 (t80) REVERT: A 4268 MET cc_start: 0.5962 (mmp) cc_final: 0.5734 (tpt) REVERT: A 4707 MET cc_start: 0.8253 (ttp) cc_final: 0.7888 (ttm) REVERT: F 58 LYS cc_start: 0.8315 (mtmp) cc_final: 0.8099 (ttpp) REVERT: I 73 MET cc_start: 0.8557 (ttp) cc_final: 0.8056 (tmm) REVERT: I 125 MET cc_start: 0.7590 (mpt) cc_final: 0.7262 (mpm) REVERT: I 146 MET cc_start: 0.0434 (ptt) cc_final: -0.0263 (pmm) REVERT: D 42 PHE cc_start: 0.8397 (t80) cc_final: 0.8170 (t80) REVERT: D 241 MET cc_start: 0.6316 (mmt) cc_final: 0.5940 (mmp) REVERT: D 317 MET cc_start: 0.7608 (ptt) cc_final: 0.7342 (ptt) REVERT: D 399 MET cc_start: 0.7845 (pmm) cc_final: 0.7408 (tmm) REVERT: D 885 LEU cc_start: 0.9585 (mt) cc_final: 0.9352 (mm) REVERT: D 935 MET cc_start: 0.8375 (ptm) cc_final: 0.7988 (ptm) REVERT: D 1062 TYR cc_start: 0.4470 (OUTLIER) cc_final: 0.2682 (m-80) REVERT: D 1165 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: D 1300 MET cc_start: 0.8549 (mmm) cc_final: 0.8252 (mmp) REVERT: D 1494 MET cc_start: 0.8562 (ppp) cc_final: 0.8230 (ppp) REVERT: D 1975 MET cc_start: 0.8262 (ptp) cc_final: 0.8032 (ptp) REVERT: D 2150 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7675 (mtt) REVERT: D 2279 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: D 2605 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: D 2662 PHE cc_start: 0.8879 (m-80) cc_final: 0.8643 (m-10) REVERT: D 2666 LEU cc_start: 0.9260 (tt) cc_final: 0.8972 (pp) REVERT: D 2695 MET cc_start: 0.8106 (mpt) cc_final: 0.7125 (mmt) REVERT: D 2719 TYR cc_start: 0.8397 (t80) cc_final: 0.7967 (t80) REVERT: D 2724 TYR cc_start: 0.8934 (t80) cc_final: 0.8165 (t80) REVERT: D 2734 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: D 2844 MET cc_start: 0.9069 (ppp) cc_final: 0.8691 (ppp) REVERT: D 2870 LEU cc_start: 0.8981 (mt) cc_final: 0.8740 (mm) REVERT: D 2880 LYS cc_start: 0.9074 (pmtt) cc_final: 0.8661 (ptmm) REVERT: D 2895 PHE cc_start: 0.9219 (t80) cc_final: 0.8410 (t80) REVERT: D 2983 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8503 (mm) REVERT: D 3046 MET cc_start: 0.7969 (mmm) cc_final: 0.7482 (mpm) REVERT: D 3131 TYR cc_start: 0.8404 (m-10) cc_final: 0.8153 (m-80) REVERT: D 3211 LEU cc_start: 0.8975 (tp) cc_final: 0.8598 (pt) REVERT: D 3221 LEU cc_start: 0.9056 (pt) cc_final: 0.8795 (tp) REVERT: D 3233 HIS cc_start: 0.8191 (t-90) cc_final: 0.7907 (t-90) REVERT: D 3954 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: B 309 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6593 (mmm) REVERT: B 981 MET cc_start: 0.6010 (tmm) cc_final: 0.5805 (tpp) REVERT: B 995 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7924 (tpt) REVERT: B 1948 MET cc_start: 0.7564 (mmp) cc_final: 0.7310 (mmt) REVERT: B 1975 MET cc_start: 0.8400 (ptp) cc_final: 0.7981 (ptp) REVERT: B 2456 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8903 (mmm) REVERT: B 2681 MET cc_start: 0.7725 (tpp) cc_final: 0.7338 (tpt) REVERT: B 2720 PHE cc_start: 0.9102 (t80) cc_final: 0.8695 (t80) REVERT: B 2724 TYR cc_start: 0.8905 (t80) cc_final: 0.8497 (t80) REVERT: B 2734 MET cc_start: 0.8221 (mpt) cc_final: 0.7661 (mpt) REVERT: B 2798 MET cc_start: 0.8848 (mmm) cc_final: 0.8266 (ptp) REVERT: B 2828 MET cc_start: 0.7600 (tpt) cc_final: 0.7045 (mmt) REVERT: B 2844 MET cc_start: 0.8866 (ppp) cc_final: 0.8524 (ppp) REVERT: B 2848 TYR cc_start: 0.8775 (t80) cc_final: 0.8496 (t80) REVERT: B 2867 ASN cc_start: -0.0916 (OUTLIER) cc_final: -0.1164 (p0) REVERT: B 2880 LYS cc_start: 0.9000 (mppt) cc_final: 0.8607 (mppt) REVERT: B 2884 LYS cc_start: 0.8910 (mppt) cc_final: 0.8534 (tmtp) REVERT: B 2895 PHE cc_start: 0.9218 (t80) cc_final: 0.8654 (t80) REVERT: B 2939 TYR cc_start: 0.7921 (m-80) cc_final: 0.7511 (m-80) REVERT: B 3046 MET cc_start: 0.8332 (mmm) cc_final: 0.7969 (mmm) REVERT: B 3072 MET cc_start: 0.8511 (ptp) cc_final: 0.8281 (mpt) REVERT: B 3115 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8738 (m90) REVERT: B 3214 LEU cc_start: 0.9181 (mp) cc_final: 0.8921 (mt) REVERT: B 3233 HIS cc_start: 0.8154 (t-90) cc_final: 0.7940 (t-90) REVERT: B 3235 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: B 3242 LEU cc_start: 0.9307 (mt) cc_final: 0.9062 (pp) REVERT: B 3243 CYS cc_start: 0.8825 (m) cc_final: 0.8401 (p) REVERT: B 3250 TRP cc_start: 0.9355 (t60) cc_final: 0.9115 (t60) REVERT: B 3295 TRP cc_start: 0.8890 (p-90) cc_final: 0.8628 (p-90) REVERT: B 3689 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: B 3854 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8232 (t80) REVERT: B 3981 MET cc_start: 0.8668 (tmm) cc_final: 0.8351 (ttp) REVERT: B 4268 MET cc_start: 0.6721 (ttp) cc_final: 0.6450 (mmm) REVERT: C 935 MET cc_start: 0.8818 (tmm) cc_final: 0.8507 (ppp) REVERT: C 1035 TYR cc_start: 0.8719 (t80) cc_final: 0.8485 (t80) REVERT: C 1165 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8065 (mtp) REVERT: C 1948 MET cc_start: 0.7249 (mmp) cc_final: 0.7001 (mmp) REVERT: C 2347 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8040 (mtt) REVERT: C 2585 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7819 (pmm) REVERT: C 2602 HIS cc_start: 0.7995 (p-80) cc_final: 0.7348 (p90) REVERT: C 2666 LEU cc_start: 0.9261 (tt) cc_final: 0.8925 (pp) REVERT: C 2850 ASN cc_start: 0.9150 (m-40) cc_final: 0.8504 (t0) REVERT: C 2880 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9026 (mppt) REVERT: C 2884 LYS cc_start: 0.9352 (mmpt) cc_final: 0.8872 (tmtt) REVERT: C 2939 TYR cc_start: 0.8050 (m-80) cc_final: 0.7541 (m-80) REVERT: C 2943 PHE cc_start: 0.7928 (m-10) cc_final: 0.7441 (m-10) REVERT: C 2980 LEU cc_start: 0.8935 (mm) cc_final: 0.8657 (mm) REVERT: C 3095 ASN cc_start: 0.9007 (t0) cc_final: 0.8479 (m-40) REVERT: C 3104 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7855 (tpt) REVERT: C 3121 LEU cc_start: 0.8764 (tp) cc_final: 0.8457 (mt) REVERT: C 3131 TYR cc_start: 0.8764 (m-10) cc_final: 0.8440 (m-80) REVERT: C 3223 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: C 3235 MET cc_start: 0.6987 (mtt) cc_final: 0.6367 (tpt) REVERT: C 3242 LEU cc_start: 0.9167 (mt) cc_final: 0.8706 (pp) REVERT: C 3245 TYR cc_start: 0.8369 (t80) cc_final: 0.8101 (t80) REVERT: C 3689 MET cc_start: 0.8367 (tpp) cc_final: 0.8115 (mtt) REVERT: C 4568 MET cc_start: 0.7563 (mmt) cc_final: 0.7310 (mmm) REVERT: J 1 MET cc_start: 0.6613 (mmm) cc_final: 0.6380 (tpp) REVERT: J 145 MET cc_start: 0.0979 (pmm) cc_final: 0.0326 (pp-130) REVERT: J 146 MET cc_start: -0.1384 (ptt) cc_final: -0.1949 (pp-130) REVERT: K 125 MET cc_start: 0.7632 (mpp) cc_final: 0.7271 (mpp) REVERT: K 145 MET cc_start: 0.1595 (pmm) cc_final: 0.1040 (pmm) REVERT: K 146 MET cc_start: 0.0222 (ptt) cc_final: -0.0380 (ppp) REVERT: L 37 MET cc_start: 0.9271 (mpt) cc_final: 0.8913 (pmm) REVERT: L 145 MET cc_start: 0.2521 (pmm) cc_final: 0.2241 (pmt) REVERT: L 146 MET cc_start: 0.0685 (OUTLIER) cc_final: -0.0021 (pp-130) outliers start: 111 outliers final: 56 residues processed: 1121 average time/residue: 2.0357 time to fit residues: 3320.1132 Evaluate side-chains 1136 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1053 time to evaluate : 11.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3181 TYR Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3829 VAL Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 2456 MET Chi-restraints excluded: chain B residue 2512 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2585 MET Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3223 GLU Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 1596 optimal weight: 5.9990 chunk 1052 optimal weight: 6.9990 chunk 1694 optimal weight: 10.0000 chunk 1034 optimal weight: 9.9990 chunk 803 optimal weight: 6.9990 chunk 1177 optimal weight: 30.0000 chunk 1777 optimal weight: 0.1980 chunk 1635 optimal weight: 0.8980 chunk 1415 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 1093 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN D3095 ASN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3252 HIS ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN L 43 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 146296 Z= 0.261 Angle : 0.644 20.064 197604 Z= 0.316 Chirality : 0.041 0.433 21684 Planarity : 0.004 0.111 25424 Dihedral : 5.213 87.858 19650 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 0.75 % Allowed : 10.83 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 1.03 (0.06), residues: 17776 helix: 1.64 (0.06), residues: 9092 sheet: -0.11 (0.12), residues: 1692 loop : -0.33 (0.08), residues: 6992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A3295 HIS 0.025 0.001 HIS D3034 PHE 0.067 0.001 PHE A1979 TYR 0.056 0.001 TYR D3181 ARG 0.018 0.000 ARG F 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35552 Ramachandran restraints generated. 17776 Oldfield, 0 Emsley, 17776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1060 time to evaluate : 12.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 26 HIS cc_start: 0.9045 (OUTLIER) cc_final: 0.8231 (t-90) REVERT: H 67 MET cc_start: 0.8830 (ttm) cc_final: 0.8557 (mtp) REVERT: A 198 ASN cc_start: 0.7631 (p0) cc_final: 0.7345 (p0) REVERT: A 393 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6112 (mmm) REVERT: A 545 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7565 (tpp80) REVERT: A 892 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8939 (mt) REVERT: A 938 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: A 940 LEU cc_start: 0.9451 (mp) cc_final: 0.9228 (pt) REVERT: A 1948 MET cc_start: 0.7218 (mmp) cc_final: 0.6968 (mmp) REVERT: A 1975 MET cc_start: 0.8312 (ptp) cc_final: 0.8065 (ptp) REVERT: A 2214 MET cc_start: 0.8888 (mmp) cc_final: 0.8634 (mmm) REVERT: A 2585 MET cc_start: 0.8114 (pmm) cc_final: 0.7819 (pmm) REVERT: A 2662 PHE cc_start: 0.8831 (m-10) cc_final: 0.8437 (m-80) REVERT: A 2688 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.2920 (pp-130) REVERT: A 2719 TYR cc_start: 0.8412 (t80) cc_final: 0.8026 (t80) REVERT: A 2734 MET cc_start: 0.8172 (mmm) cc_final: 0.7843 (mpt) REVERT: A 2844 MET cc_start: 0.8853 (ppp) cc_final: 0.8466 (ppp) REVERT: A 2850 ASN cc_start: 0.9195 (m-40) cc_final: 0.8417 (t0) REVERT: A 2880 LYS cc_start: 0.8827 (mppt) cc_final: 0.8577 (mppt) REVERT: A 3046 MET cc_start: 0.8308 (mpp) cc_final: 0.7516 (mpp) REVERT: A 3101 LEU cc_start: 0.9059 (mm) cc_final: 0.8432 (tm) REVERT: A 3123 LEU cc_start: 0.9033 (mt) cc_final: 0.8786 (mm) REVERT: A 3131 TYR cc_start: 0.8513 (m-10) cc_final: 0.8193 (m-80) REVERT: A 3159 LEU cc_start: 0.8867 (mt) cc_final: 0.8393 (mp) REVERT: A 3235 MET cc_start: 0.6826 (mmt) cc_final: 0.6603 (mmt) REVERT: A 3263 MET cc_start: 0.4894 (ppp) cc_final: 0.4423 (pmm) REVERT: A 3298 ARG cc_start: 0.8658 (ptm160) cc_final: 0.8242 (ptm160) REVERT: A 3323 MET cc_start: 0.7624 (mpm) cc_final: 0.7314 (mpm) REVERT: A 3605 MET cc_start: 0.2970 (tmm) cc_final: 0.2507 (tpt) REVERT: A 4035 TYR cc_start: 0.7802 (m-80) cc_final: 0.7477 (t80) REVERT: A 4268 MET cc_start: 0.5971 (mmp) cc_final: 0.5731 (tpt) REVERT: A 4707 MET cc_start: 0.8264 (ttp) cc_final: 0.7892 (ttm) REVERT: F 26 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8764 (t-90) REVERT: F 58 LYS cc_start: 0.8312 (mtmp) cc_final: 0.8096 (ttpp) REVERT: I 64 ILE cc_start: 0.8286 (pp) cc_final: 0.8082 (pt) REVERT: I 73 MET cc_start: 0.8591 (ttp) cc_final: 0.8120 (tmm) REVERT: I 77 MET cc_start: 0.8973 (tmm) cc_final: 0.8504 (tmm) REVERT: I 125 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7318 (mpm) REVERT: I 142 PHE cc_start: 0.6976 (t80) cc_final: 0.6735 (t80) REVERT: I 146 MET cc_start: 0.0363 (ptt) cc_final: -0.0118 (pmm) REVERT: D 42 PHE cc_start: 0.8399 (t80) cc_final: 0.8172 (t80) REVERT: D 241 MET cc_start: 0.6327 (mmt) cc_final: 0.6109 (mpm) REVERT: D 317 MET cc_start: 0.7628 (ptt) cc_final: 0.7356 (ptt) REVERT: D 399 MET cc_start: 0.7846 (pmm) cc_final: 0.7413 (tmm) REVERT: D 885 LEU cc_start: 0.9585 (mt) cc_final: 0.9353 (mm) REVERT: D 935 MET cc_start: 0.8378 (ptm) cc_final: 0.7991 (ptm) REVERT: D 1062 TYR cc_start: 0.4462 (OUTLIER) cc_final: 0.2691 (m-80) REVERT: D 1165 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7997 (mtt) REVERT: D 1300 MET cc_start: 0.8555 (mmm) cc_final: 0.8240 (mmt) REVERT: D 1494 MET cc_start: 0.8526 (ppp) cc_final: 0.8187 (ppp) REVERT: D 1975 MET cc_start: 0.8270 (ptp) cc_final: 0.8038 (ptp) REVERT: D 2150 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7699 (mtt) REVERT: D 2279 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: D 2468 MET cc_start: 0.8745 (mmt) cc_final: 0.8348 (mmt) REVERT: D 2590 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8260 (ttp80) REVERT: D 2605 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8525 (ttp) REVERT: D 2662 PHE cc_start: 0.8894 (m-80) cc_final: 0.8652 (m-10) REVERT: D 2666 LEU cc_start: 0.9275 (tt) cc_final: 0.8988 (pp) REVERT: D 2695 MET cc_start: 0.8104 (mpt) cc_final: 0.7132 (mmt) REVERT: D 2719 TYR cc_start: 0.8413 (t80) cc_final: 0.8000 (t80) REVERT: D 2724 TYR cc_start: 0.8907 (t80) cc_final: 0.8102 (t80) REVERT: D 2734 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7390 (mtt) REVERT: D 2870 LEU cc_start: 0.8993 (mt) cc_final: 0.8756 (mm) REVERT: D 2880 LYS cc_start: 0.9087 (pmtt) cc_final: 0.8673 (ptmm) REVERT: D 2895 PHE cc_start: 0.9201 (t80) cc_final: 0.8357 (t80) REVERT: D 2983 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 3046 MET cc_start: 0.7974 (mmm) cc_final: 0.7511 (mpm) REVERT: D 3131 TYR cc_start: 0.8407 (m-10) cc_final: 0.8154 (m-80) REVERT: D 3211 LEU cc_start: 0.8968 (tp) cc_final: 0.8601 (pt) REVERT: D 3221 LEU cc_start: 0.9006 (pt) cc_final: 0.8758 (tp) REVERT: D 3233 HIS cc_start: 0.8174 (t-90) cc_final: 0.7877 (t-90) REVERT: D 3323 MET cc_start: 0.7033 (mpm) cc_final: 0.5396 (ptm) REVERT: D 3954 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: B 309 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6593 (mmm) REVERT: B 995 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7928 (tpt) REVERT: B 1948 MET cc_start: 0.7530 (mmp) cc_final: 0.7298 (mmt) REVERT: B 1975 MET cc_start: 0.8419 (ptp) cc_final: 0.8011 (ptp) REVERT: B 2456 MET cc_start: 0.9145 (mmt) cc_final: 0.8924 (mmm) REVERT: B 2681 MET cc_start: 0.7821 (tpp) cc_final: 0.7438 (tpt) REVERT: B 2720 PHE cc_start: 0.9060 (t80) cc_final: 0.8751 (t80) REVERT: B 2724 TYR cc_start: 0.8921 (t80) cc_final: 0.8510 (t80) REVERT: B 2734 MET cc_start: 0.8222 (mpt) cc_final: 0.7656 (mpt) REVERT: B 2798 MET cc_start: 0.8835 (mmm) cc_final: 0.8224 (ptp) REVERT: B 2828 MET cc_start: 0.7621 (tpt) cc_final: 0.7060 (mmt) REVERT: B 2844 MET cc_start: 0.8845 (ppp) cc_final: 0.8498 (ppp) REVERT: B 2848 TYR cc_start: 0.8771 (t80) cc_final: 0.8495 (t80) REVERT: B 2867 ASN cc_start: -0.0693 (OUTLIER) cc_final: -0.0940 (p0) REVERT: B 2880 LYS cc_start: 0.8994 (mppt) cc_final: 0.8630 (mppt) REVERT: B 2884 LYS cc_start: 0.8919 (mppt) cc_final: 0.8555 (tmtp) REVERT: B 2895 PHE cc_start: 0.9229 (t80) cc_final: 0.8669 (t80) REVERT: B 2939 TYR cc_start: 0.7925 (m-80) cc_final: 0.7504 (m-80) REVERT: B 2941 LEU cc_start: 0.9012 (pt) cc_final: 0.8547 (mm) REVERT: B 3046 MET cc_start: 0.8345 (mmm) cc_final: 0.7981 (mmm) REVERT: B 3072 MET cc_start: 0.8514 (ptp) cc_final: 0.8219 (mpt) REVERT: B 3115 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (m90) REVERT: B 3214 LEU cc_start: 0.9191 (mp) cc_final: 0.8924 (mt) REVERT: B 3233 HIS cc_start: 0.8220 (t-90) cc_final: 0.7988 (t-90) REVERT: B 3235 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: B 3242 LEU cc_start: 0.9311 (mt) cc_final: 0.8978 (pp) REVERT: B 3243 CYS cc_start: 0.8825 (m) cc_final: 0.8006 (m) REVERT: B 3250 TRP cc_start: 0.9353 (t60) cc_final: 0.9099 (t60) REVERT: B 3295 TRP cc_start: 0.8882 (p-90) cc_final: 0.8647 (p-90) REVERT: B 3689 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: B 3719 MET cc_start: 0.8047 (tpp) cc_final: 0.7794 (tpt) REVERT: B 3854 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8196 (t80) REVERT: B 3981 MET cc_start: 0.8647 (tmm) cc_final: 0.8333 (ttp) REVERT: B 4268 MET cc_start: 0.6663 (ttp) cc_final: 0.6419 (mmm) REVERT: C 895 MET cc_start: 0.7386 (mmt) cc_final: 0.6967 (mmt) REVERT: C 935 MET cc_start: 0.8820 (tmm) cc_final: 0.8515 (ppp) REVERT: C 981 MET cc_start: 0.5874 (ppp) cc_final: 0.5626 (tmm) REVERT: C 1035 TYR cc_start: 0.8734 (t80) cc_final: 0.8493 (t80) REVERT: C 1165 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: C 1948 MET cc_start: 0.7190 (mmp) cc_final: 0.6887 (mmp) REVERT: C 2347 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: C 2585 MET cc_start: 0.8295 (ppp) cc_final: 0.7796 (pmm) REVERT: C 2602 HIS cc_start: 0.8007 (p-80) cc_final: 0.7381 (p90) REVERT: C 2666 LEU cc_start: 0.9281 (tt) cc_final: 0.8947 (pp) REVERT: C 2828 MET cc_start: 0.7093 (tpt) cc_final: 0.6731 (tpt) REVERT: C 2850 ASN cc_start: 0.9153 (m-40) cc_final: 0.8507 (t0) REVERT: C 2880 LYS cc_start: 0.9307 (mmtm) cc_final: 0.9082 (mppt) REVERT: C 2884 LYS cc_start: 0.9352 (mmpt) cc_final: 0.8871 (tmtt) REVERT: C 2890 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8720 (mp10) REVERT: C 2939 TYR cc_start: 0.8061 (m-80) cc_final: 0.7585 (m-80) REVERT: C 2943 PHE cc_start: 0.7917 (m-10) cc_final: 0.7431 (m-10) REVERT: C 2980 LEU cc_start: 0.8935 (mm) cc_final: 0.8652 (mm) REVERT: C 3095 ASN cc_start: 0.9012 (t0) cc_final: 0.8480 (m-40) REVERT: C 3104 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7881 (tpt) REVERT: C 3131 TYR cc_start: 0.8772 (m-10) cc_final: 0.8403 (m-80) REVERT: C 3215 MET cc_start: 0.9304 (mpp) cc_final: 0.8873 (pmm) REVERT: C 3223 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: C 3235 MET cc_start: 0.7081 (mtt) cc_final: 0.6772 (mpp) REVERT: C 3242 LEU cc_start: 0.9146 (mt) cc_final: 0.8605 (pp) REVERT: C 3245 TYR cc_start: 0.8420 (t80) cc_final: 0.8183 (t80) REVERT: C 3246 MET cc_start: 0.8797 (ttp) cc_final: 0.8067 (mtp) REVERT: C 3689 MET cc_start: 0.8391 (tpp) cc_final: 0.8120 (mtt) REVERT: C 4568 MET cc_start: 0.7579 (mmt) cc_final: 0.7326 (mmm) REVERT: C 4707 MET cc_start: 0.8380 (ttm) cc_final: 0.8106 (ttt) REVERT: J 1 MET cc_start: 0.6681 (mmm) cc_final: 0.6422 (tpp) REVERT: J 52 MET cc_start: 0.8778 (ppp) cc_final: 0.8389 (pmm) REVERT: J 145 MET cc_start: 0.1050 (pmm) cc_final: 0.0367 (pp-130) REVERT: J 146 MET cc_start: -0.1500 (ptt) cc_final: -0.2035 (pp-130) REVERT: K 125 MET cc_start: 0.7620 (mpp) cc_final: 0.7257 (mpp) REVERT: K 145 MET cc_start: 0.1610 (pmm) cc_final: 0.0971 (pmm) REVERT: K 146 MET cc_start: 0.0085 (ptt) cc_final: -0.0490 (ppp) REVERT: L 1 MET cc_start: 0.6847 (mmp) cc_final: 0.6536 (mmp) REVERT: L 37 MET cc_start: 0.9287 (mpt) cc_final: 0.8938 (pmm) REVERT: L 76 LYS cc_start: 0.8892 (pttm) cc_final: 0.8562 (ptpt) REVERT: L 77 MET cc_start: 0.8825 (tpp) cc_final: 0.8535 (tmm) REVERT: L 145 MET cc_start: 0.2555 (pmm) cc_final: 0.2287 (pmt) REVERT: L 146 MET cc_start: 0.0691 (OUTLIER) cc_final: 0.0068 (pp-130) outliers start: 110 outliers final: 58 residues processed: 1112 average time/residue: 2.0688 time to fit residues: 3351.0335 Evaluate side-chains 1138 residues out of total 15696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1051 time to evaluate : 12.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 2384 MET Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2700 ASN Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3268 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4183 LYS Chi-restraints excluded: chain A residue 4752 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1973 ILE Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2279 MET Chi-restraints excluded: chain D residue 2396 ILE Chi-restraints excluded: chain D residue 2605 MET Chi-restraints excluded: chain D residue 2700 ASN Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2887 GLU Chi-restraints excluded: chain D residue 2983 LEU Chi-restraints excluded: chain D residue 3021 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3115 HIS Chi-restraints excluded: chain D residue 3181 TYR Chi-restraints excluded: chain D residue 3680 CYS Chi-restraints excluded: chain D residue 3829 VAL Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 3954 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2512 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2700 ASN Chi-restraints excluded: chain B residue 2867 ASN Chi-restraints excluded: chain B residue 2887 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 3021 LEU Chi-restraints excluded: chain B residue 3115 HIS Chi-restraints excluded: chain B residue 3235 MET Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 938 GLU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1501 ASN Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2347 MET Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2448 ASP Chi-restraints excluded: chain C residue 2700 ASN Chi-restraints excluded: chain C residue 2890 GLN Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3115 HIS Chi-restraints excluded: chain C residue 3201 VAL Chi-restraints excluded: chain C residue 3207 ASN Chi-restraints excluded: chain C residue 3223 GLU Chi-restraints excluded: chain C residue 3299 LEU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 139 TYR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1784 random chunks: chunk 867 optimal weight: 5.9990 chunk 1124 optimal weight: 3.9990 chunk 1507 optimal weight: 0.9980 chunk 433 optimal weight: 0.9990 chunk 1304 optimal weight: 0.0980 chunk 208 optimal weight: 2.9990 chunk 393 optimal weight: 5.9990 chunk 1417 optimal weight: 0.0970 chunk 593 optimal weight: 4.9990 chunk 1455 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2867 ASN D3095 ASN D4488 GLN B 395 HIS ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2684 ASN ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3286 ASN ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3252 HIS ** J 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 9 GLN L 43 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.058614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.043981 restraints weight = 1281894.478| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.66 r_work: 0.3046 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 146296 Z= 0.169 Angle : 0.625 20.453 197604 Z= 0.305 Chirality : 0.040 0.431 21684 Planarity : 0.004 0.110 25424 Dihedral : 5.079 88.019 19650 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 0.70 % Allowed : 10.95 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 1.11 (0.06), residues: 17776 helix: 1.71 (0.06), residues: 9060 sheet: -0.12 (0.12), residues: 1712 loop : -0.26 (0.08), residues: 7004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A3295 HIS 0.022 0.001 HIS D3034 PHE 0.039 0.001 PHE J 69 TYR 0.044 0.001 TYR C2719 ARG 0.020 0.000 ARG F 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53155.55 seconds wall clock time: 919 minutes 57.64 seconds (55197.64 seconds total)