Starting phenix.real_space_refine on Mon Mar 18 16:37:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxc_42759/03_2024/8uxc_42759_updated.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88204 2.51 5 N 23588 2.21 5 O 25844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A ASP 1194": "OD1" <-> "OD2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2186": "OE1" <-> "OE2" Residue "A PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2591": "NH1" <-> "NH2" Residue "A TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2769": "OE1" <-> "OE2" Residue "A ASP 2944": "OD1" <-> "OD2" Residue "A TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2972": "OD1" <-> "OD2" Residue "A GLU 3124": "OE1" <-> "OE2" Residue "A TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4073": "OD1" <-> "OD2" Residue "A ASP 4093": "OD1" <-> "OD2" Residue "A GLU 4151": "OE1" <-> "OE2" Residue "A GLU 4562": "OE1" <-> "OE2" Residue "A TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B GLU 1001": "OE1" <-> "OE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B ASP 1194": "OD1" <-> "OD2" Residue "B ASP 1199": "OD1" <-> "OD2" Residue "B GLU 1634": "OE1" <-> "OE2" Residue "B PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2186": "OE1" <-> "OE2" Residue "B PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2591": "NH1" <-> "NH2" Residue "B TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2769": "OE1" <-> "OE2" Residue "B ASP 2944": "OD1" <-> "OD2" Residue "B TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2972": "OD1" <-> "OD2" Residue "B GLU 3124": "OE1" <-> "OE2" Residue "B TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4073": "OD1" <-> "OD2" Residue "B ASP 4093": "OD1" <-> "OD2" Residue "B GLU 4151": "OE1" <-> "OE2" Residue "B GLU 4562": "OE1" <-> "OE2" Residue "B TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 378": "OD1" <-> "OD2" Residue "C PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C GLU 1001": "OE1" <-> "OE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1131": "OD1" <-> "OD2" Residue "C ASP 1194": "OD1" <-> "OD2" Residue "C ASP 1199": "OD1" <-> "OD2" Residue "C GLU 1634": "OE1" <-> "OE2" Residue "C PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2186": "OE1" <-> "OE2" Residue "C PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2591": "NH1" <-> "NH2" Residue "C TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2769": "OE1" <-> "OE2" Residue "C ASP 2944": "OD1" <-> "OD2" Residue "C TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2972": "OD1" <-> "OD2" Residue "C GLU 3124": "OE1" <-> "OE2" Residue "C TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4073": "OD1" <-> "OD2" Residue "C ASP 4093": "OD1" <-> "OD2" Residue "C GLU 4151": "OE1" <-> "OE2" Residue "C GLU 4562": "OE1" <-> "OE2" Residue "C TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D GLU 1001": "OE1" <-> "OE2" Residue "D PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D ASP 1194": "OD1" <-> "OD2" Residue "D ASP 1199": "OD1" <-> "OD2" Residue "D GLU 1634": "OE1" <-> "OE2" Residue "D PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2186": "OE1" <-> "OE2" Residue "D PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2591": "NH1" <-> "NH2" Residue "D TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2769": "OE1" <-> "OE2" Residue "D ASP 2944": "OD1" <-> "OD2" Residue "D TYR 2956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2972": "OD1" <-> "OD2" Residue "D GLU 3124": "OE1" <-> "OE2" Residue "D TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4073": "OD1" <-> "OD2" Residue "D ASP 4093": "OD1" <-> "OD2" Residue "D GLU 4151": "OE1" <-> "OE2" Residue "D GLU 4562": "OE1" <-> "OE2" Residue "D TYR 4661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4951": "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: 138600 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "C" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "D" Number of atoms: 33769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33761 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34483 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33090 SG CYS A4888 177.363 203.534 87.507 1.00127.42 S ATOM 33115 SG CYS A4891 179.878 203.251 90.370 1.00119.44 S ATOM 70131 SG CYS B4888 175.586 177.341 87.520 1.00128.71 S ATOM 70156 SG CYS B4891 175.871 179.855 90.383 1.00125.31 S ATOM A030C SG CYS C4888 201.752 175.581 87.519 1.00128.95 S ATOM A0311 SG CYS C4891 199.237 175.866 90.382 1.00122.88 S ATOM A0T2D SG CYS D4888 203.510 201.746 87.511 1.00130.29 S ATOM A0T32 SG CYS D4891 203.225 199.232 90.374 1.00122.16 S Time building chain proxies: 95.86, per 1000 atoms: 0.69 Number of scatterers: 138600 At special positions: 0 Unit cell: (379.925, 379.925, 210.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 936 16.00 P 24 15.00 O 25844 8.00 N 23588 7.00 C 88204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.10 Conformation dependent library (CDL) restraints added in 35.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 700 helices and 92 sheets defined 59.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 37.80 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 5.475A pdb=" N SER A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.759A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.586A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.980A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.532A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.660A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.535A pdb=" N VAL A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.597A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.811A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.703A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.683A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.580A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.606A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.601A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.541A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 875 through 901 removed outlier: 5.015A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 removed outlier: 3.525A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix No H-bonds generated for 'chain 'A' and resid 920 through 925' Processing helix chain 'A' and resid 926 through 947 removed outlier: 3.835A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.734A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 4.837A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.064A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.920A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.110A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.847A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.707A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1503 removed outlier: 3.991A pdb=" N ASN A1502 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1503' Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 4.074A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.236A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.889A 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: 3.702A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.798A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1722 Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.553A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.317A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.686A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1955 removed outlier: 4.269A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1965 removed outlier: 3.582A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 5.687A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 4.994A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.547A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.713A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2152 Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2166 removed outlier: 3.688A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2182 removed outlier: 3.630A pdb=" N VAL A2178 " --> pdb=" O VAL A2174 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.506A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 3.658A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 removed outlier: 3.580A 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: 3.682A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.568A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.527A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.033A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.583A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.744A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.640A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.233A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 3.629A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.152A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2618 Proline residue: A2606 - end of helix removed outlier: 3.834A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.199A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 removed outlier: 3.644A pdb=" N LEU A2666 " --> pdb=" O PHE A2662 " (cutoff:3.500A) Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 3.735A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2740 removed outlier: 4.774A pdb=" N TYR A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.463A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 3.887A pdb=" N GLU A2769 " --> pdb=" O GLU A2765 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.228A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.380A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2950 removed outlier: 3.531A pdb=" N SER A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY A2945 " --> pdb=" O LEU A2941 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY A2946 " --> pdb=" O GLU A2942 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A2949 " --> pdb=" O GLY A2945 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS A2950 " --> pdb=" O GLY A2946 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.606A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.500A 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: 5.162A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3078 removed outlier: 3.715A pdb=" N LEU A3068 " --> pdb=" O ALA A3064 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.894A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.100A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A3139 " --> pdb=" O THR A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3150 removed outlier: 4.109A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3151 through 3166 removed outlier: 3.652A pdb=" N LEU A3155 " --> pdb=" O GLN A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.211A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3172 through 3180' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.694A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.972A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.812A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.070A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 removed outlier: 3.741A pdb=" N ASN A3257 " --> pdb=" O GLY A3253 " (cutoff:3.500A) Proline residue: A3258 - end of helix No H-bonds generated for 'chain 'A' and resid 3253 through 3258' Processing helix chain 'A' and resid 3269 through 3291 removed outlier: 4.285A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3311 removed outlier: 4.425A pdb=" N ARG A3298 " --> pdb=" O ALA A3294 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.363A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3330 removed outlier: 5.364A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 3.805A pdb=" N ALA A3330 " --> pdb=" O LEU A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3605 Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.951A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.857A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.729A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.941A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.473A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3826 through 3848 removed outlier: 5.277A pdb=" N LEU A3830 " --> pdb=" O GLY A3826 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A3831 " --> pdb=" O GLU A3827 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A3832 " --> pdb=" O LYS A3828 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP A3833 " --> pdb=" O VAL A3829 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A3834 " --> pdb=" O LEU A3830 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A3835 " --> pdb=" O GLN A3831 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.578A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.699A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3959 removed outlier: 3.656A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.740A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 removed outlier: 3.700A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.372A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.161A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.728A 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: 3.549A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (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: 4.782A pdb=" N MET A4186 " --> pdb=" O GLU A4182 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4258 removed outlier: 4.180A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) Processing helix chain 'A' and resid 4264 through 4272 Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.743A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.444A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.317A 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: 3.985A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.671A 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 4673 through 4683 removed outlier: 6.063A pdb=" N LEU A4677 " --> pdb=" O ASP A4673 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 6.060A 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: 3.797A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4750 removed outlier: 4.742A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.909A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.408A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.426A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4832 removed outlier: 4.132A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU A4832 " --> pdb=" O GLY A4828 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.884A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 3.732A 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: 4.892A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.481A 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 'B' and resid 51 through 56 removed outlier: 5.475A pdb=" N SER B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.759A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.587A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.981A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.532A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.660A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.535A pdb=" N VAL B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.596A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.811A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.703A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 3.683A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.580A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.606A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.600A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 619 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.542A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 875 through 901 removed outlier: 5.015A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.524A pdb=" N LEU B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Proline residue: B 925 - end of helix No H-bonds generated for 'chain 'B' and resid 920 through 925' Processing helix chain 'B' and resid 926 through 947 removed outlier: 3.834A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.734A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 4.837A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.065A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 3.919A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.110A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.846A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.707A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1503 removed outlier: 3.992A pdb=" N ASN B1502 " --> pdb=" O GLN B1498 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1498 through 1503' Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 4.074A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.237A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.497A 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: 4.890A 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: 3.703A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B1666 " --> pdb=" O SER B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.798A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1722 Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.552A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.317A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.686A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1955 removed outlier: 4.268A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1965 removed outlier: 3.582A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 5.688A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 4.995A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.546A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.713A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2152 Processing helix chain 'B' and resid 2153 through 2158 Processing helix chain 'B' and resid 2159 through 2166 removed outlier: 3.688A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2182 removed outlier: 3.631A pdb=" N VAL B2178 " --> pdb=" O VAL B2174 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.505A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 3.657A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 removed outlier: 3.580A 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: 3.683A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.568A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.527A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.033A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.582A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.744A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.640A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.234A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 3.630A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.152A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2602 through 2618 Proline residue: B2606 - end of helix removed outlier: 3.835A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.200A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 removed outlier: 3.644A pdb=" N LEU B2666 " --> pdb=" O PHE B2662 " (cutoff:3.500A) Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 3.734A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) Processing helix chain 'B' and resid 2715 through 2740 removed outlier: 4.774A pdb=" N TYR B2719 " --> pdb=" O GLU B2715 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.464A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 3.887A pdb=" N GLU B2769 " --> pdb=" O GLU B2765 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.228A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.380A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2950 removed outlier: 3.531A pdb=" N SER B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY B2945 " --> pdb=" O LEU B2941 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B2946 " --> pdb=" O GLU B2942 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B2949 " --> pdb=" O GLY B2945 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS B2950 " --> pdb=" O GLY B2946 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.605A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.501A 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: 5.161A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3078 removed outlier: 3.716A pdb=" N LEU B3068 " --> pdb=" O ALA B3064 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.892A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.100A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B3139 " --> pdb=" O THR B3135 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3150 removed outlier: 4.109A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3151 through 3166 removed outlier: 3.652A pdb=" N LEU B3155 " --> pdb=" O GLN B3151 " (cutoff:3.500A) Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.211A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3172 through 3180' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.692A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.972A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.812A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.070A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 removed outlier: 3.741A pdb=" N ASN B3257 " --> pdb=" O GLY B3253 " (cutoff:3.500A) Proline residue: B3258 - end of helix No H-bonds generated for 'chain 'B' and resid 3253 through 3258' Processing helix chain 'B' and resid 3269 through 3291 removed outlier: 4.285A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3294 through 3311 removed outlier: 4.426A pdb=" N ARG B3298 " --> pdb=" O ALA B3294 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.362A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3330 removed outlier: 5.364A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 3.805A pdb=" N ALA B3330 " --> pdb=" O LEU B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3605 Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.951A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.858A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.729A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.941A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.473A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3826 through 3848 removed outlier: 5.277A pdb=" N LEU B3830 " --> pdb=" O GLY B3826 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B3831 " --> pdb=" O GLU B3827 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP B3832 " --> pdb=" O LYS B3828 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B3833 " --> pdb=" O VAL B3829 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU B3834 " --> pdb=" O LEU B3830 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B3835 " --> pdb=" O GLN B3831 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.579A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.698A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3959 removed outlier: 3.654A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.740A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 removed outlier: 3.701A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.373A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.162A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.726A 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: 3.550A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (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: 4.782A pdb=" N MET B4186 " --> pdb=" O GLU B4182 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4258 removed outlier: 4.181A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) Processing helix chain 'B' and resid 4264 through 4272 Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.744A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.443A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.318A 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: 3.985A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.672A 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 4673 through 4683 removed outlier: 6.063A pdb=" N LEU B4677 " --> pdb=" O ASP B4673 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 6.061A 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: 3.798A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4750 removed outlier: 4.743A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.910A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.408A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.425A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4832 removed outlier: 4.132A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU B4832 " --> pdb=" O GLY B4828 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.884A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 3.732A 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: 4.892A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.481A 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 51 through 56 removed outlier: 5.475A pdb=" N SER C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.759A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.586A pdb=" N ALA C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 224' Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.979A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.533A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.660A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.534A pdb=" N VAL C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 446' Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.596A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.811A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.702A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.683A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.580A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.606A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.601A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.542A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 875 through 901 removed outlier: 5.016A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 removed outlier: 3.523A pdb=" N LEU C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Proline residue: C 925 - end of helix No H-bonds generated for 'chain 'C' and resid 920 through 925' Processing helix chain 'C' and resid 926 through 947 removed outlier: 3.834A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.734A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 4.837A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.064A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 3.919A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.110A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.847A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.707A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1498 through 1503 removed outlier: 3.992A pdb=" N ASN C1502 " --> pdb=" O GLN C1498 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1498 through 1503' Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 4.074A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.237A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.889A 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: 3.703A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C1666 " --> pdb=" O SER C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.797A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1722 Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.552A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.317A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.686A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1955 removed outlier: 4.268A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1965 removed outlier: 3.581A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 5.687A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 4.994A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.547A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.713A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2152 Processing helix chain 'C' and resid 2153 through 2158 Processing helix chain 'C' and resid 2159 through 2166 removed outlier: 3.689A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2182 removed outlier: 3.630A pdb=" N VAL C2178 " --> pdb=" O VAL C2174 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.505A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 3.658A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 removed outlier: 3.580A 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: 3.682A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.567A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.526A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.034A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.583A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.744A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.640A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.233A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 3.630A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.153A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2602 through 2618 Proline residue: C2606 - end of helix removed outlier: 3.835A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.199A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 removed outlier: 3.644A pdb=" N LEU C2666 " --> pdb=" O PHE C2662 " (cutoff:3.500A) Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 3.735A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) Processing helix chain 'C' and resid 2715 through 2740 removed outlier: 4.773A pdb=" N TYR C2719 " --> pdb=" O GLU C2715 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.464A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 3.887A pdb=" N GLU C2769 " --> pdb=" O GLU C2765 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.228A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.380A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2950 removed outlier: 3.532A pdb=" N SER C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY C2945 " --> pdb=" O LEU C2941 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C2946 " --> pdb=" O GLU C2942 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C2949 " --> pdb=" O GLY C2945 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS C2950 " --> pdb=" O GLY C2946 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.606A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.500A 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: 5.161A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3078 removed outlier: 3.715A pdb=" N LEU C3068 " --> pdb=" O ALA C3064 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.893A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.100A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C3139 " --> pdb=" O THR C3135 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3150 removed outlier: 4.109A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3151 through 3166 removed outlier: 3.651A pdb=" N LEU C3155 " --> pdb=" O GLN C3151 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.211A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3172 through 3180' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.693A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.973A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.812A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.071A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 removed outlier: 3.740A pdb=" N ASN C3257 " --> pdb=" O GLY C3253 " (cutoff:3.500A) Proline residue: C3258 - end of helix No H-bonds generated for 'chain 'C' and resid 3253 through 3258' Processing helix chain 'C' and resid 3269 through 3291 removed outlier: 4.286A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3294 through 3311 removed outlier: 4.426A pdb=" N ARG C3298 " --> pdb=" O ALA C3294 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.363A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3330 removed outlier: 5.364A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 3.805A pdb=" N ALA C3330 " --> pdb=" O LEU C3326 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3605 Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.951A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.858A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.729A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.942A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.473A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3826 through 3848 removed outlier: 5.277A pdb=" N LEU C3830 " --> pdb=" O GLY C3826 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN C3831 " --> pdb=" O GLU C3827 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C3832 " --> pdb=" O LYS C3828 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP C3833 " --> pdb=" O VAL C3829 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C3834 " --> pdb=" O LEU C3830 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C3835 " --> pdb=" O GLN C3831 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.579A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.698A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3959 removed outlier: 3.655A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.740A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 removed outlier: 3.700A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.373A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.162A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.728A 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: 3.549A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (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: 4.782A pdb=" N MET C4186 " --> pdb=" O GLU C4182 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4258 removed outlier: 4.180A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) Processing helix chain 'C' and resid 4264 through 4272 Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.744A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.443A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.318A 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: 3.985A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.672A 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 4673 through 4683 removed outlier: 6.063A pdb=" N LEU C4677 " --> pdb=" O ASP C4673 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 6.061A 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: 3.797A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4750 removed outlier: 4.742A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.909A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.407A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.426A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4832 removed outlier: 4.133A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU C4832 " --> pdb=" O GLY C4828 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.884A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 3.732A 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: 4.891A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.481A 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 'D' and resid 51 through 56 removed outlier: 5.476A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.759A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.587A pdb=" N ALA D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 224' Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.980A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.533A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.660A pdb=" N LEU D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.535A pdb=" N VAL D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 446' Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.596A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.811A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.702A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 563 removed outlier: 3.684A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.580A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.606A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.601A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 619 " --> pdb=" O CYS D 615 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.542A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 875 through 901 removed outlier: 5.015A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 925 removed outlier: 3.524A pdb=" N LEU D 924 " --> pdb=" O GLU D 920 " (cutoff:3.500A) Proline residue: D 925 - end of helix No H-bonds generated for 'chain 'D' and resid 920 through 925' Processing helix chain 'D' and resid 926 through 947 removed outlier: 3.834A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.733A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 4.837A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.064A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 3.920A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.110A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.847A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.707A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1498 through 1503 removed outlier: 3.992A pdb=" N ASN D1502 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1498 through 1503' Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 4.074A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.237A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.889A 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: 3.703A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D1666 " --> pdb=" O SER D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.798A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1722 Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.552A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.317A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.685A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1955 removed outlier: 4.268A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1965 removed outlier: 3.582A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 5.687A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 4.994A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.547A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.712A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2152 Processing helix chain 'D' and resid 2153 through 2158 Processing helix chain 'D' and resid 2159 through 2166 removed outlier: 3.689A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2182 removed outlier: 3.630A pdb=" N VAL D2178 " --> pdb=" O VAL D2174 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.506A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 3.657A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 removed outlier: 3.580A 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: 3.683A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.567A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.526A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.033A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.582A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.745A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.639A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.234A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 3.630A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.153A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2602 through 2618 Proline residue: D2606 - end of helix removed outlier: 3.834A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.199A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 removed outlier: 3.644A pdb=" N LEU D2666 " --> pdb=" O PHE D2662 " (cutoff:3.500A) Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 3.736A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) Processing helix chain 'D' and resid 2715 through 2740 removed outlier: 4.773A pdb=" N TYR D2719 " --> pdb=" O GLU D2715 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.465A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 3.887A pdb=" N GLU D2769 " --> pdb=" O GLU D2765 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.228A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.380A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2950 removed outlier: 3.530A pdb=" N SER D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY D2945 " --> pdb=" O LEU D2941 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY D2946 " --> pdb=" O GLU D2942 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D2949 " --> pdb=" O GLY D2945 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS D2950 " --> pdb=" O GLY D2946 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.605A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.501A 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: 5.161A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3078 removed outlier: 3.715A pdb=" N LEU D3068 " --> pdb=" O ALA D3064 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.893A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.100A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D3139 " --> pdb=" O THR D3135 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3150 removed outlier: 4.108A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3151 through 3166 removed outlier: 3.651A pdb=" N LEU D3155 " --> pdb=" O GLN D3151 " (cutoff:3.500A) Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.211A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3172 through 3180' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.692A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.973A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.812A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.070A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 removed outlier: 3.742A pdb=" N ASN D3257 " --> pdb=" O GLY D3253 " (cutoff:3.500A) Proline residue: D3258 - end of helix No H-bonds generated for 'chain 'D' and resid 3253 through 3258' Processing helix chain 'D' and resid 3269 through 3291 removed outlier: 4.285A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3294 through 3311 removed outlier: 4.426A pdb=" N ARG D3298 " --> pdb=" O ALA D3294 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.363A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3330 removed outlier: 5.364A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 3.804A pdb=" N ALA D3330 " --> pdb=" O LEU D3326 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3605 Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.950A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.857A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.729A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.941A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.472A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3826 through 3848 removed outlier: 5.277A pdb=" N LEU D3830 " --> pdb=" O GLY D3826 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D3831 " --> pdb=" O GLU D3827 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP D3832 " --> pdb=" O LYS D3828 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP D3833 " --> pdb=" O VAL D3829 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU D3834 " --> pdb=" O LEU D3830 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE D3835 " --> pdb=" O GLN D3831 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.578A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.699A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3959 removed outlier: 3.656A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.740A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 removed outlier: 3.700A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.373A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.162A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.728A 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: 3.549A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (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: 4.781A pdb=" N MET D4186 " --> pdb=" O GLU D4182 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4258 removed outlier: 4.180A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) Processing helix chain 'D' and resid 4264 through 4272 Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.743A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.443A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.317A 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: 3.985A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.672A 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 4673 through 4683 removed outlier: 6.062A pdb=" N LEU D4677 " --> pdb=" O ASP D4673 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 6.061A 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: 3.797A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4750 removed outlier: 4.742A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.909A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.407A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.426A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4832 removed outlier: 4.133A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU D4832 " --> pdb=" O GLY D4828 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.884A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.891A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.481A 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 'E' and resid 39 through 44 removed outlier: 3.642A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.737A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.267A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.642A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 3.736A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.266A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.642A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.737A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 4.267A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.642A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.737A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.267A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 5.324A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.154A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.720A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 128 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 160 through 165 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= 5, first strand: chain 'A' and resid 260 through 264 removed outlier: 5.245A pdb=" N LEU A 236 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N VAL A 247 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 15.020A pdb=" N LEU A 234 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.269A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 8, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 9, first strand: chain 'A' and resid 737 through 740 removed outlier: 5.549A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.715A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A1621 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 776 through 780 removed outlier: 5.429A pdb=" N GLN A 776 " --> pdb=" O GLY A1470 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.200A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 948 through 952 removed outlier: 3.850A pdb=" N HIS A 949 " --> pdb=" O GLU A1065 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 951 " --> pdb=" O ASN A1063 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 3.597A pdb=" N GLY A1019 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 7.000A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.554A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A1433 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.803A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2741 through 2744 Processing sheet with id= 19, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 4.029A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.709A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 22, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.324A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.155A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.720A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 160 through 165 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 26, first strand: chain 'B' and resid 260 through 264 removed outlier: 5.244A pdb=" N LEU B 236 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N VAL B 247 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 15.020A pdb=" N LEU B 234 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.269A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 29, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 30, first strand: chain 'B' and resid 737 through 740 removed outlier: 5.549A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.714A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B1621 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.428A pdb=" N GLN B 776 " --> pdb=" O GLY B1470 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.200A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 948 through 952 removed outlier: 3.850A pdb=" N HIS B 949 " --> pdb=" O GLU B1065 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 951 " --> pdb=" O ASN B1063 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 3.597A pdb=" N GLY B1019 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 6.999A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.554A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B1433 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.802A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2741 through 2744 Processing sheet with id= 40, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 4.029A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.710A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 43, first strand: chain 'C' and resid 47 through 50 removed outlier: 5.324A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.154A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.720A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 160 through 165 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 47, first strand: chain 'C' and resid 260 through 264 removed outlier: 5.246A pdb=" N LEU C 236 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N VAL C 247 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 15.019A pdb=" N LEU C 234 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.268A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 50, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 51, first strand: chain 'C' and resid 737 through 740 removed outlier: 5.549A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.715A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C1621 " --> pdb=" O ILE C 798 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.429A pdb=" N GLN C 776 " --> pdb=" O GLY C1470 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.200A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 948 through 952 removed outlier: 3.850A pdb=" N HIS C 949 " --> pdb=" O GLU C1065 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 951 " --> pdb=" O ASN C1063 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 3.596A pdb=" N GLY C1019 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 7.001A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.554A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C1433 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.801A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 2741 through 2744 Processing sheet with id= 61, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 4.029A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.709A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 64, first strand: chain 'D' and resid 47 through 50 removed outlier: 5.324A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.154A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.720A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 160 through 165 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 68, first strand: chain 'D' and resid 260 through 264 removed outlier: 5.245A pdb=" N LEU D 236 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N VAL D 247 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 15.019A pdb=" N LEU D 234 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.269A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 71, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 72, first strand: chain 'D' and resid 737 through 740 removed outlier: 5.549A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.714A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS D1621 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 776 through 780 removed outlier: 5.429A pdb=" N GLN D 776 " --> pdb=" O GLY D1470 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.199A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 948 through 952 removed outlier: 3.850A pdb=" N HIS D 949 " --> pdb=" O GLU D1065 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 951 " --> pdb=" O ASN D1063 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 3.596A pdb=" N GLY D1019 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 6.999A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.555A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D1433 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.802A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 2741 through 2744 Processing sheet with id= 82, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 4.028A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.709A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 85, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.432A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'E' and resid 46 through 51 removed outlier: 4.971A pdb=" N GLN E 21 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.433A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'F' and resid 46 through 51 removed outlier: 4.970A pdb=" N GLN F 21 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.433A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'G' and resid 46 through 51 removed outlier: 4.971A pdb=" N GLN G 21 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.433A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.970A pdb=" N GLN H 21 " --> pdb=" O ILE H 51 " (cutoff:3.500A) 7356 hydrogen bonds defined for protein. 21952 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: 93.69 Time building geometry restraints manager: 45.67 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: 45376 1.34 - 1.46: 32323 1.46 - 1.58: 62377 1.58 - 1.70: 32 1.70 - 1.82: 1512 Bond restraints: 141620 Sorted by residual: bond pdb=" CA GLU B4179 " pdb=" CB GLU B4179 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.53e-02 4.27e+03 8.09e+00 bond pdb=" CA GLU D4179 " pdb=" CB GLU D4179 " ideal model delta sigma weight residual 1.526 1.569 -0.043 1.53e-02 4.27e+03 7.77e+00 bond pdb=" CA GLU C4179 " pdb=" CB GLU C4179 " ideal model delta sigma weight residual 1.526 1.569 -0.043 1.53e-02 4.27e+03 7.75e+00 bond pdb=" CA GLU A4179 " pdb=" CB GLU A4179 " ideal model delta sigma weight residual 1.526 1.569 -0.043 1.53e-02 4.27e+03 7.75e+00 bond pdb=" CA LEU B2165 " pdb=" C LEU B2165 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.38e-02 5.25e+03 5.38e+00 ... (remaining 141615 not shown) Histogram of bond angle deviations from ideal: 94.61 - 103.68: 1957 103.68 - 112.75: 75020 112.75 - 121.82: 85507 121.82 - 130.89: 28111 130.89 - 139.96: 753 Bond angle restraints: 191348 Sorted by residual: angle pdb=" CB MET A3072 " pdb=" CG MET A3072 " pdb=" SD MET A3072 " ideal model delta sigma weight residual 112.70 94.61 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET B3072 " pdb=" CG MET B3072 " pdb=" SD MET B3072 " ideal model delta sigma weight residual 112.70 94.62 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET C3072 " pdb=" CG MET C3072 " pdb=" SD MET C3072 " ideal model delta sigma weight residual 112.70 94.62 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET D3072 " pdb=" CG MET D3072 " pdb=" SD MET D3072 " ideal model delta sigma weight residual 112.70 94.62 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET B3235 " pdb=" CG MET B3235 " pdb=" SD MET B3235 " ideal model delta sigma weight residual 112.70 97.09 15.61 3.00e+00 1.11e-01 2.71e+01 ... (remaining 191343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 77250 17.71 - 35.41: 6568 35.41 - 53.12: 1100 53.12 - 70.83: 342 70.83 - 88.53: 144 Dihedral angle restraints: 85404 sinusoidal: 35044 harmonic: 50360 Sorted by residual: dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual -180.00 -131.50 -48.50 0 5.00e+00 4.00e-02 9.41e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual 180.00 -131.50 -48.50 0 5.00e+00 4.00e-02 9.41e+01 dihedral pdb=" CA PHE C4640 " pdb=" C PHE C4640 " pdb=" N PRO C4641 " pdb=" CA PRO C4641 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.40e+01 ... (remaining 85401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 19281 0.072 - 0.144: 1640 0.144 - 0.217: 52 0.217 - 0.289: 11 0.289 - 0.361: 4 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CG LEU A3276 " pdb=" CB LEU A3276 " pdb=" CD1 LEU A3276 " pdb=" CD2 LEU A3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CG LEU D3276 " pdb=" CB LEU D3276 " pdb=" CD1 LEU D3276 " pdb=" CD2 LEU D3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CG LEU B3276 " pdb=" CB LEU B3276 " pdb=" CD1 LEU B3276 " pdb=" CD2 LEU B3276 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.115 5.00e-02 4.00e+02 1.78e-01 5.07e+01 pdb=" N PRO A4641 " -0.308 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.115 5.00e-02 4.00e+02 1.78e-01 5.07e+01 pdb=" N PRO C4641 " -0.308 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " 0.115 5.00e-02 4.00e+02 1.78e-01 5.06e+01 pdb=" N PRO D4641 " -0.308 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " 0.087 5.00e-02 4.00e+02 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 2361 2.69 - 3.24: 139987 3.24 - 3.80: 229848 3.80 - 4.35: 305897 4.35 - 4.90: 493753 Nonbonded interactions: 1171846 Sorted by model distance: nonbonded pdb=" OE2 GLU C 920 " pdb=" OG SER C 922 " model vdw 2.139 2.440 nonbonded pdb=" OE2 GLU B 920 " pdb=" OG SER B 922 " model vdw 2.140 2.440 nonbonded pdb=" OE2 GLU A 920 " pdb=" OG SER A 922 " model vdw 2.140 2.440 nonbonded pdb=" OE2 GLU D 920 " pdb=" OG SER D 922 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR D4897 " pdb=" OE2 GLU D4963 " model vdw 2.144 2.440 ... (remaining 1171841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 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: 0.170 Extract box with map and model: 30.960 Check model and map are aligned: 1.530 Set scattering table: 1.030 Process input model: 430.180 Find NCS groups from input model: 7.600 Set up NCS constraints: 0.950 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 489.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 141620 Z= 0.173 Angle : 0.672 19.208 191348 Z= 0.386 Chirality : 0.040 0.361 20988 Planarity : 0.005 0.178 24588 Dihedral : 14.098 88.535 52928 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.06), residues: 17212 helix: 1.71 (0.06), residues: 8956 sheet: 0.07 (0.13), residues: 1568 loop : -0.42 (0.07), residues: 6688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 893 HIS 0.027 0.001 HIS A2168 PHE 0.061 0.001 PHE C4640 TYR 0.056 0.001 TYR D3285 ARG 0.007 0.000 ARG B2788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 817 time to evaluate : 12.264 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 995 MET cc_start: 0.8624 (tpt) cc_final: 0.7986 (tpp) REVERT: A 2685 TYR cc_start: 0.8157 (t80) cc_final: 0.7438 (t80) REVERT: A 2757 MET cc_start: 0.8924 (mpp) cc_final: 0.8380 (mpt) REVERT: A 2779 LEU cc_start: 0.9389 (mm) cc_final: 0.9124 (mt) REVERT: A 2843 MET cc_start: 0.8705 (mtm) cc_final: 0.8187 (ptp) REVERT: A 3072 MET cc_start: 0.9249 (mtt) cc_final: 0.8842 (mpp) REVERT: A 3147 TYR cc_start: 0.8211 (m-80) cc_final: 0.7986 (m-80) REVERT: A 3817 LEU cc_start: 0.8646 (mp) cc_final: 0.8407 (mp) REVERT: A 4306 PHE cc_start: 0.7756 (m-80) cc_final: 0.7194 (m-80) REVERT: E 58 LYS cc_start: 0.8479 (ptpp) cc_final: 0.8094 (pmmt) REVERT: F 58 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8068 (pmmt) REVERT: G 58 LYS cc_start: 0.8548 (ptpp) cc_final: 0.8185 (pmmt) REVERT: B 995 MET cc_start: 0.8621 (tpt) cc_final: 0.7921 (tpp) REVERT: B 2685 TYR cc_start: 0.8137 (t80) cc_final: 0.7249 (t80) REVERT: B 2757 MET cc_start: 0.8805 (mpp) cc_final: 0.8238 (mpt) REVERT: B 2779 LEU cc_start: 0.9442 (mm) cc_final: 0.9202 (mt) REVERT: B 2843 MET cc_start: 0.8695 (mtm) cc_final: 0.8177 (ptp) REVERT: B 3072 MET cc_start: 0.9208 (mtt) cc_final: 0.8929 (mpp) REVERT: B 3147 TYR cc_start: 0.8185 (m-80) cc_final: 0.7963 (m-80) REVERT: B 3817 LEU cc_start: 0.8644 (mp) cc_final: 0.8409 (mp) REVERT: B 4306 PHE cc_start: 0.7734 (m-80) cc_final: 0.7175 (m-80) REVERT: C 995 MET cc_start: 0.8606 (tpt) cc_final: 0.7912 (tpp) REVERT: C 2685 TYR cc_start: 0.8171 (t80) cc_final: 0.7286 (t80) REVERT: C 2757 MET cc_start: 0.8803 (mpp) cc_final: 0.8263 (mpt) REVERT: C 2779 LEU cc_start: 0.9431 (mm) cc_final: 0.9193 (mt) REVERT: C 2843 MET cc_start: 0.8714 (mtm) cc_final: 0.8190 (ptp) REVERT: C 3072 MET cc_start: 0.9174 (mtt) cc_final: 0.8910 (mpp) REVERT: C 3147 TYR cc_start: 0.8160 (m-80) cc_final: 0.7943 (m-80) REVERT: C 3817 LEU cc_start: 0.8642 (mp) cc_final: 0.8407 (mp) REVERT: C 4306 PHE cc_start: 0.7752 (m-80) cc_final: 0.7195 (m-80) REVERT: D 995 MET cc_start: 0.8634 (tpt) cc_final: 0.7950 (tpp) REVERT: D 2685 TYR cc_start: 0.8159 (t80) cc_final: 0.7352 (t80) REVERT: D 2757 MET cc_start: 0.8807 (mpp) cc_final: 0.8268 (mpt) REVERT: D 2779 LEU cc_start: 0.9438 (mm) cc_final: 0.9194 (mt) REVERT: D 2843 MET cc_start: 0.8765 (mtm) cc_final: 0.8210 (ptp) REVERT: D 3072 MET cc_start: 0.9206 (mtt) cc_final: 0.8926 (mpp) REVERT: D 3147 TYR cc_start: 0.8177 (m-80) cc_final: 0.7948 (m-80) REVERT: D 3817 LEU cc_start: 0.8656 (mp) cc_final: 0.8416 (mp) REVERT: D 4306 PHE cc_start: 0.7745 (m-80) cc_final: 0.7182 (m-80) outliers start: 4 outliers final: 0 residues processed: 817 average time/residue: 2.1512 time to fit residues: 2492.7012 Evaluate side-chains 741 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 741 time to evaluate : 11.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 10.0000 chunk 1309 optimal weight: 9.9990 chunk 726 optimal weight: 10.0000 chunk 447 optimal weight: 9.9990 chunk 883 optimal weight: 9.9990 chunk 699 optimal weight: 0.7980 chunk 1354 optimal weight: 10.0000 chunk 524 optimal weight: 8.9990 chunk 823 optimal weight: 7.9990 chunk 1008 optimal weight: 5.9990 chunk 1569 optimal weight: 20.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 HIS A1793 GLN A1974 ASN ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2890 GLN A2937 HIS ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3233 HIS ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4787 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1267 HIS B1793 GLN B1974 ASN ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2890 GLN B2937 HIS ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3233 HIS ** B3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1267 HIS C1793 GLN ** C1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1974 ASN ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2802 ASN C2937 HIS ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3233 HIS ** C3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1267 HIS D1793 GLN D1974 ASN ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2890 GLN D2937 HIS ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3233 HIS ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 141620 Z= 0.435 Angle : 0.653 15.109 191348 Z= 0.335 Chirality : 0.044 0.222 20988 Planarity : 0.005 0.162 24588 Dihedral : 5.945 89.003 19024 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 0.40 % Allowed : 4.35 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.06), residues: 17212 helix: 1.84 (0.06), residues: 9000 sheet: -0.15 (0.13), residues: 1576 loop : -0.37 (0.07), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 893 HIS 0.011 0.001 HIS C3732 PHE 0.047 0.002 PHE C4640 TYR 0.047 0.002 TYR A3285 ARG 0.013 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 786 time to evaluate : 12.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.8651 (tpt) cc_final: 0.8056 (tpp) REVERT: A 2584 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8136 (mmt) REVERT: A 2779 LEU cc_start: 0.9523 (mm) cc_final: 0.9282 (mt) REVERT: A 2835 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7806 (mmm160) REVERT: A 2843 MET cc_start: 0.8780 (mtm) cc_final: 0.8189 (mtp) REVERT: A 2844 MET cc_start: 0.8547 (tmt) cc_final: 0.8213 (tmt) REVERT: A 3072 MET cc_start: 0.9190 (mtt) cc_final: 0.8722 (mtt) REVERT: A 3147 TYR cc_start: 0.8309 (m-80) cc_final: 0.8059 (m-80) REVERT: A 3719 MET cc_start: 0.8132 (tpp) cc_final: 0.7856 (tpt) REVERT: A 3819 MET cc_start: 0.7630 (mtt) cc_final: 0.6991 (mpp) REVERT: A 4306 PHE cc_start: 0.7769 (m-80) cc_final: 0.7243 (m-80) REVERT: A 4748 MET cc_start: 0.7093 (mpt) cc_final: 0.6763 (mpt) REVERT: E 4 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7811 (tm-30) REVERT: E 6 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 18 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8848 (mtmm) REVERT: E 30 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7402 (mtm) REVERT: F 4 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7763 (tm-30) REVERT: F 6 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7595 (mm-30) REVERT: F 30 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7437 (mtm) REVERT: F 108 GLU cc_start: 0.8440 (pp20) cc_final: 0.8233 (pp20) REVERT: G 30 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7424 (mtm) REVERT: H 30 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7419 (mtm) REVERT: H 108 GLU cc_start: 0.8425 (pp20) cc_final: 0.8207 (pp20) REVERT: B 981 MET cc_start: 0.7578 (ppp) cc_final: 0.7093 (tmm) REVERT: B 995 MET cc_start: 0.8678 (tpt) cc_final: 0.7984 (tpp) REVERT: B 2150 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: B 2584 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8185 (mmt) REVERT: B 2779 LEU cc_start: 0.9561 (mm) cc_final: 0.9334 (mt) REVERT: B 2843 MET cc_start: 0.8778 (mtm) cc_final: 0.8182 (mtp) REVERT: B 2844 MET cc_start: 0.8522 (tmt) cc_final: 0.8190 (tmt) REVERT: B 3147 TYR cc_start: 0.8292 (m-80) cc_final: 0.8034 (m-80) REVERT: B 3719 MET cc_start: 0.8133 (tpp) cc_final: 0.7862 (tpt) REVERT: B 3819 MET cc_start: 0.7575 (mtt) cc_final: 0.6939 (mpp) REVERT: B 4306 PHE cc_start: 0.7727 (m-80) cc_final: 0.7243 (m-80) REVERT: C 678 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8240 (tpt) REVERT: C 981 MET cc_start: 0.7569 (ppp) cc_final: 0.7095 (tmm) REVERT: C 995 MET cc_start: 0.8659 (tpt) cc_final: 0.8001 (tpp) REVERT: C 999 LEU cc_start: 0.9114 (tp) cc_final: 0.8844 (tm) REVERT: C 2150 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7419 (mpp) REVERT: C 2584 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: C 2779 LEU cc_start: 0.9553 (mm) cc_final: 0.9326 (mt) REVERT: C 2843 MET cc_start: 0.8795 (mtm) cc_final: 0.8177 (mtp) REVERT: C 2844 MET cc_start: 0.8518 (tmt) cc_final: 0.8190 (tmt) REVERT: C 3147 TYR cc_start: 0.8276 (m-80) cc_final: 0.8030 (m-80) REVERT: C 3719 MET cc_start: 0.8129 (tpp) cc_final: 0.7857 (tpt) REVERT: C 3819 MET cc_start: 0.7584 (mtt) cc_final: 0.6952 (mpp) REVERT: C 4306 PHE cc_start: 0.7742 (m-80) cc_final: 0.7233 (m-80) REVERT: D 678 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8212 (tpt) REVERT: D 981 MET cc_start: 0.7601 (ppp) cc_final: 0.7107 (tmm) REVERT: D 995 MET cc_start: 0.8681 (tpt) cc_final: 0.8043 (tpp) REVERT: D 999 LEU cc_start: 0.9112 (tp) cc_final: 0.8844 (tm) REVERT: D 2150 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: D 2584 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8151 (mmt) REVERT: D 2779 LEU cc_start: 0.9562 (mm) cc_final: 0.9331 (mt) REVERT: D 2835 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7841 (mmm160) REVERT: D 2843 MET cc_start: 0.8850 (mtm) cc_final: 0.8210 (mtp) REVERT: D 2844 MET cc_start: 0.8561 (tmt) cc_final: 0.8226 (tmt) REVERT: D 3147 TYR cc_start: 0.8298 (m-80) cc_final: 0.8034 (m-80) REVERT: D 3719 MET cc_start: 0.8141 (tpp) cc_final: 0.7860 (tpt) REVERT: D 3819 MET cc_start: 0.7586 (mtt) cc_final: 0.6954 (mpp) REVERT: D 4306 PHE cc_start: 0.7744 (m-80) cc_final: 0.7235 (m-80) outliers start: 60 outliers final: 5 residues processed: 792 average time/residue: 2.1307 time to fit residues: 2409.0472 Evaluate side-chains 766 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 748 time to evaluate : 12.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2584 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 4075 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.7980 chunk 487 optimal weight: 10.0000 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 1572 optimal weight: 0.7980 chunk 1698 optimal weight: 8.9990 chunk 1400 optimal weight: 10.0000 chunk 1558 optimal weight: 8.9990 chunk 535 optimal weight: 8.9990 chunk 1261 optimal weight: 9.9990 overall best weight: 5.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2802 ASN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2890 GLN ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1939 ASN ** D1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 141620 Z= 0.365 Angle : 0.615 19.237 191348 Z= 0.313 Chirality : 0.042 0.206 20988 Planarity : 0.005 0.151 24588 Dihedral : 5.823 88.344 19024 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.52 % Allowed : 5.66 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.06), residues: 17212 helix: 1.87 (0.06), residues: 9028 sheet: -0.17 (0.12), residues: 1728 loop : -0.36 (0.07), residues: 6456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D2732 HIS 0.010 0.001 HIS A3732 PHE 0.031 0.002 PHE A4640 TYR 0.043 0.002 TYR B2801 ARG 0.014 0.001 ARG H 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 786 time to evaluate : 12.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (tpt) REVERT: A 981 MET cc_start: 0.7802 (ppp) cc_final: 0.7486 (tmm) REVERT: A 995 MET cc_start: 0.8676 (tpt) cc_final: 0.8063 (tpp) REVERT: A 2584 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8128 (mmt) REVERT: A 2685 TYR cc_start: 0.7795 (t80) cc_final: 0.7112 (t80) REVERT: A 2779 LEU cc_start: 0.9557 (mm) cc_final: 0.9320 (mt) REVERT: A 2843 MET cc_start: 0.8818 (mtm) cc_final: 0.8370 (ptp) REVERT: A 2844 MET cc_start: 0.8683 (tmt) cc_final: 0.7100 (tmm) REVERT: A 3003 MET cc_start: 0.8725 (mtp) cc_final: 0.8499 (mtm) REVERT: A 3147 TYR cc_start: 0.8276 (m-80) cc_final: 0.8001 (m-80) REVERT: A 3689 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7823 (mpp) REVERT: A 3719 MET cc_start: 0.8123 (tpp) cc_final: 0.7842 (tpt) REVERT: A 3819 MET cc_start: 0.7667 (mtt) cc_final: 0.7139 (mpp) REVERT: A 3854 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8930 (t80) REVERT: A 4161 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 4306 PHE cc_start: 0.7786 (m-80) cc_final: 0.7246 (m-80) REVERT: A 4748 MET cc_start: 0.7076 (mpt) cc_final: 0.6858 (mpt) REVERT: E 6 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7671 (mt-10) REVERT: E 18 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8888 (mtmm) REVERT: E 30 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7434 (mtm) REVERT: E 50 ARG cc_start: 0.8690 (mtm110) cc_final: 0.8411 (mtp180) REVERT: E 53 LYS cc_start: 0.9339 (mmtm) cc_final: 0.9086 (mmtm) REVERT: F 4 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7864 (tm-30) REVERT: F 6 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7646 (mt-10) REVERT: G 30 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: G 53 LYS cc_start: 0.9368 (mmtp) cc_final: 0.9141 (mmtm) REVERT: H 30 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: H 50 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8368 (mtp85) REVERT: H 108 GLU cc_start: 0.8493 (pp20) cc_final: 0.8281 (pp20) REVERT: B 995 MET cc_start: 0.8708 (tpt) cc_final: 0.7998 (tpp) REVERT: B 2584 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8135 (mmt) REVERT: B 2779 LEU cc_start: 0.9589 (mm) cc_final: 0.9360 (mt) REVERT: B 2843 MET cc_start: 0.8825 (mtm) cc_final: 0.8353 (ptp) REVERT: B 2844 MET cc_start: 0.8662 (tmt) cc_final: 0.7105 (tmm) REVERT: B 3003 MET cc_start: 0.8697 (mtp) cc_final: 0.8459 (mtm) REVERT: B 3072 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: B 3147 TYR cc_start: 0.8269 (m-80) cc_final: 0.7981 (m-80) REVERT: B 3689 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7815 (mpp) REVERT: B 3719 MET cc_start: 0.8127 (tpp) cc_final: 0.7846 (tpt) REVERT: B 3819 MET cc_start: 0.7609 (mtt) cc_final: 0.7090 (mpp) REVERT: B 3854 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8925 (t80) REVERT: B 4161 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: B 4306 PHE cc_start: 0.7755 (m-80) cc_final: 0.7226 (m-80) REVERT: C 995 MET cc_start: 0.8680 (tpt) cc_final: 0.8012 (tpp) REVERT: C 2584 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8112 (mmt) REVERT: C 2779 LEU cc_start: 0.9581 (mm) cc_final: 0.9354 (mt) REVERT: C 2843 MET cc_start: 0.8837 (mtm) cc_final: 0.8354 (ptp) REVERT: C 2844 MET cc_start: 0.8670 (tmt) cc_final: 0.7122 (tmm) REVERT: C 3003 MET cc_start: 0.8689 (mtp) cc_final: 0.8463 (mtm) REVERT: C 3072 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8795 (mtm) REVERT: C 3147 TYR cc_start: 0.8266 (m-80) cc_final: 0.7989 (m-80) REVERT: C 3689 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: C 3719 MET cc_start: 0.8121 (tpp) cc_final: 0.7846 (tpt) REVERT: C 3819 MET cc_start: 0.7600 (mtt) cc_final: 0.7073 (mpp) REVERT: C 3854 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8928 (t80) REVERT: C 4161 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: C 4306 PHE cc_start: 0.7763 (m-80) cc_final: 0.7237 (m-80) REVERT: D 995 MET cc_start: 0.8702 (tpt) cc_final: 0.8027 (tpp) REVERT: D 2584 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8123 (mmt) REVERT: D 2779 LEU cc_start: 0.9588 (mm) cc_final: 0.9355 (mt) REVERT: D 2843 MET cc_start: 0.8887 (mtm) cc_final: 0.8393 (ptp) REVERT: D 2844 MET cc_start: 0.8715 (tmt) cc_final: 0.7167 (tmm) REVERT: D 3003 MET cc_start: 0.8676 (mtp) cc_final: 0.8451 (mtm) REVERT: D 3072 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8821 (mtm) REVERT: D 3147 TYR cc_start: 0.8285 (m-80) cc_final: 0.7991 (m-80) REVERT: D 3689 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7802 (mpp) REVERT: D 3719 MET cc_start: 0.8131 (tpp) cc_final: 0.7852 (tpt) REVERT: D 3819 MET cc_start: 0.7615 (mtt) cc_final: 0.7087 (mpp) REVERT: D 3854 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8934 (t80) REVERT: D 4161 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: D 4306 PHE cc_start: 0.7773 (m-80) cc_final: 0.7250 (m-80) outliers start: 79 outliers final: 15 residues processed: 807 average time/residue: 2.1564 time to fit residues: 2486.7715 Evaluate side-chains 801 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 763 time to evaluate : 12.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2584 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 7.9990 chunk 1181 optimal weight: 30.0000 chunk 815 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 750 optimal weight: 10.0000 chunk 1055 optimal weight: 10.0000 chunk 1577 optimal weight: 20.0000 chunk 1670 optimal weight: 2.9990 chunk 824 optimal weight: 1.9990 chunk 1495 optimal weight: 10.0000 chunk 450 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 HIS A1939 ASN ** A1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3998 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 ASN ** B1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3998 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 ASN ** C1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2937 HIS ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3998 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 141620 Z= 0.351 Angle : 0.615 16.766 191348 Z= 0.312 Chirality : 0.042 0.325 20988 Planarity : 0.005 0.144 24588 Dihedral : 5.710 89.261 19024 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 0.69 % Allowed : 6.44 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.06), residues: 17212 helix: 1.89 (0.05), residues: 9020 sheet: -0.17 (0.12), residues: 1716 loop : -0.36 (0.07), residues: 6476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B2773 HIS 0.009 0.001 HIS D3732 PHE 0.032 0.002 PHE A2943 TYR 0.046 0.002 TYR C2801 ARG 0.014 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 780 time to evaluate : 12.464 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 995 MET cc_start: 0.8679 (tpt) cc_final: 0.7973 (tpp) REVERT: A 2584 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8089 (mmt) REVERT: A 2685 TYR cc_start: 0.7432 (t80) cc_final: 0.7211 (t80) REVERT: A 2779 LEU cc_start: 0.9435 (mm) cc_final: 0.9188 (mt) REVERT: A 2840 MET cc_start: 0.8835 (mmt) cc_final: 0.8093 (mmt) REVERT: A 2843 MET cc_start: 0.8847 (mtm) cc_final: 0.8338 (ptp) REVERT: A 2844 MET cc_start: 0.8613 (tmt) cc_final: 0.6924 (tmm) REVERT: A 3003 MET cc_start: 0.8739 (mtp) cc_final: 0.8488 (mtt) REVERT: A 3072 MET cc_start: 0.9053 (mmm) cc_final: 0.8835 (mmm) REVERT: A 3147 TYR cc_start: 0.8292 (m-80) cc_final: 0.7989 (m-80) REVERT: A 3689 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7795 (mpp) REVERT: A 3719 MET cc_start: 0.8109 (tpp) cc_final: 0.7856 (tpt) REVERT: A 3819 MET cc_start: 0.7680 (mtt) cc_final: 0.7282 (mpp) REVERT: A 3854 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8951 (t80) REVERT: A 4161 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 4306 PHE cc_start: 0.7787 (m-80) cc_final: 0.7257 (m-80) REVERT: A 4748 MET cc_start: 0.7077 (mpt) cc_final: 0.6761 (mpt) REVERT: E 18 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8802 (mtmm) REVERT: E 50 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8423 (mtp180) REVERT: E 53 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9104 (mmtm) REVERT: F 6 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7683 (mt-10) REVERT: G 50 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8426 (mtp85) REVERT: G 108 GLU cc_start: 0.8510 (pp20) cc_final: 0.8309 (pp20) REVERT: B 995 MET cc_start: 0.8704 (tpt) cc_final: 0.7959 (tpp) REVERT: B 2150 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7208 (mpp) REVERT: B 2685 TYR cc_start: 0.7797 (t80) cc_final: 0.7255 (t80) REVERT: B 2779 LEU cc_start: 0.9457 (mm) cc_final: 0.9219 (mt) REVERT: B 2840 MET cc_start: 0.8770 (mmt) cc_final: 0.7994 (mmt) REVERT: B 2843 MET cc_start: 0.8843 (mtm) cc_final: 0.8354 (ptp) REVERT: B 2844 MET cc_start: 0.8588 (tmt) cc_final: 0.6715 (tmm) REVERT: B 2860 LEU cc_start: 0.9128 (pp) cc_final: 0.8828 (tm) REVERT: B 3003 MET cc_start: 0.8718 (mtp) cc_final: 0.8493 (mtm) REVERT: B 3072 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8770 (mtm) REVERT: B 3147 TYR cc_start: 0.8264 (m-80) cc_final: 0.7985 (m-80) REVERT: B 3689 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7809 (mpp) REVERT: B 3719 MET cc_start: 0.8120 (tpp) cc_final: 0.7858 (tpt) REVERT: B 3819 MET cc_start: 0.7622 (mtt) cc_final: 0.7234 (mpp) REVERT: B 3854 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8951 (t80) REVERT: B 4161 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: B 4306 PHE cc_start: 0.7795 (m-80) cc_final: 0.7262 (m-80) REVERT: C 349 MET cc_start: 0.8607 (mmt) cc_final: 0.8407 (mmt) REVERT: C 678 MET cc_start: 0.8398 (mmm) cc_final: 0.8048 (tpp) REVERT: C 995 MET cc_start: 0.8686 (tpt) cc_final: 0.7998 (tpp) REVERT: C 2150 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7203 (mpp) REVERT: C 2685 TYR cc_start: 0.7755 (t80) cc_final: 0.7213 (t80) REVERT: C 2779 LEU cc_start: 0.9447 (mm) cc_final: 0.9210 (mt) REVERT: C 2840 MET cc_start: 0.8775 (mmt) cc_final: 0.7992 (mmt) REVERT: C 2843 MET cc_start: 0.8856 (mtm) cc_final: 0.8338 (ptp) REVERT: C 2844 MET cc_start: 0.8588 (tmt) cc_final: 0.6905 (tmm) REVERT: C 3003 MET cc_start: 0.8709 (mtp) cc_final: 0.8494 (mtm) REVERT: C 3072 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8751 (mtm) REVERT: C 3147 TYR cc_start: 0.8247 (m-80) cc_final: 0.7946 (m-80) REVERT: C 3689 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7811 (mpp) REVERT: C 3719 MET cc_start: 0.8116 (tpp) cc_final: 0.7862 (tpt) REVERT: C 3819 MET cc_start: 0.7631 (mtt) cc_final: 0.7243 (mpp) REVERT: C 3854 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8952 (t80) REVERT: C 4161 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: C 4306 PHE cc_start: 0.7798 (m-80) cc_final: 0.7265 (m-80) REVERT: D 678 MET cc_start: 0.8370 (mmm) cc_final: 0.8019 (tpp) REVERT: D 995 MET cc_start: 0.8723 (tpt) cc_final: 0.7980 (tpp) REVERT: D 2150 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7204 (mpp) REVERT: D 2584 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8099 (mmt) REVERT: D 2685 TYR cc_start: 0.7728 (t80) cc_final: 0.6972 (t80) REVERT: D 2779 LEU cc_start: 0.9497 (mm) cc_final: 0.9250 (mt) REVERT: D 2840 MET cc_start: 0.8842 (mmt) cc_final: 0.8065 (mmt) REVERT: D 2843 MET cc_start: 0.8919 (mtm) cc_final: 0.8384 (ptp) REVERT: D 2844 MET cc_start: 0.8624 (tmt) cc_final: 0.7004 (tmm) REVERT: D 2860 LEU cc_start: 0.9169 (pp) cc_final: 0.8855 (tm) REVERT: D 3003 MET cc_start: 0.8688 (mtp) cc_final: 0.8481 (mtm) REVERT: D 3072 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8702 (mtt) REVERT: D 3147 TYR cc_start: 0.8262 (m-80) cc_final: 0.7948 (m-80) REVERT: D 3689 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: D 3719 MET cc_start: 0.8121 (tpp) cc_final: 0.7852 (tpt) REVERT: D 3819 MET cc_start: 0.7627 (mtt) cc_final: 0.7233 (mpp) REVERT: D 3854 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8953 (t80) REVERT: D 4161 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: D 4306 PHE cc_start: 0.7786 (m-80) cc_final: 0.7258 (m-80) outliers start: 105 outliers final: 17 residues processed: 834 average time/residue: 2.1513 time to fit residues: 2567.3927 Evaluate side-chains 794 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 757 time to evaluate : 12.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2584 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 8.9990 chunk 948 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 1243 optimal weight: 0.8980 chunk 689 optimal weight: 20.0000 chunk 1425 optimal weight: 1.9990 chunk 1154 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 852 optimal weight: 4.9990 chunk 1499 optimal weight: 10.0000 chunk 421 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B2937 HIS ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2802 ASN ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C2937 HIS ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 GLN ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN D1004 HIS ** D1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 141620 Z= 0.305 Angle : 0.608 17.004 191348 Z= 0.306 Chirality : 0.041 0.356 20988 Planarity : 0.005 0.138 24588 Dihedral : 5.612 89.971 19024 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.64 % Allowed : 7.21 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.06), residues: 17212 helix: 1.92 (0.06), residues: 9040 sheet: -0.17 (0.12), residues: 1728 loop : -0.33 (0.07), residues: 6444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A2773 HIS 0.009 0.001 HIS D3732 PHE 0.019 0.001 PHE A4016 TYR 0.044 0.001 TYR B2801 ARG 0.018 0.000 ARG A2835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 776 time to evaluate : 12.446 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: A 995 MET cc_start: 0.8673 (tpt) cc_final: 0.7948 (tpp) REVERT: A 2685 TYR cc_start: 0.7707 (t80) cc_final: 0.7275 (t80) REVERT: A 2843 MET cc_start: 0.8868 (mtm) cc_final: 0.8392 (ptp) REVERT: A 2844 MET cc_start: 0.8252 (tmt) cc_final: 0.7852 (ttm) REVERT: A 2858 MET cc_start: 0.8649 (mmp) cc_final: 0.8289 (mpp) REVERT: A 3003 MET cc_start: 0.8719 (mtp) cc_final: 0.8476 (mtt) REVERT: A 3072 MET cc_start: 0.9072 (mmm) cc_final: 0.8779 (mmm) REVERT: A 3147 TYR cc_start: 0.8298 (m-80) cc_final: 0.7994 (m-80) REVERT: A 3689 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7785 (mpp) REVERT: A 3819 MET cc_start: 0.7623 (mtt) cc_final: 0.7295 (mpp) REVERT: A 3854 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8932 (t80) REVERT: A 4161 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: A 4306 PHE cc_start: 0.7796 (m-80) cc_final: 0.7277 (m-80) REVERT: A 4748 MET cc_start: 0.7050 (mpt) cc_final: 0.6731 (mpt) REVERT: E 18 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8785 (mtmm) REVERT: E 50 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8283 (mtp85) REVERT: G 50 ARG cc_start: 0.8619 (mtm110) cc_final: 0.8257 (mtp85) REVERT: G 53 LYS cc_start: 0.9325 (mmtm) cc_final: 0.9101 (mmtm) REVERT: B 678 MET cc_start: 0.8592 (tpp) cc_final: 0.7963 (ttp) REVERT: B 995 MET cc_start: 0.8695 (tpt) cc_final: 0.7947 (tpp) REVERT: B 2150 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: B 2685 TYR cc_start: 0.7717 (t80) cc_final: 0.7204 (t80) REVERT: B 2840 MET cc_start: 0.8733 (mmt) cc_final: 0.7892 (mmt) REVERT: B 2843 MET cc_start: 0.8844 (mtm) cc_final: 0.8432 (ptp) REVERT: B 2858 MET cc_start: 0.8605 (mmp) cc_final: 0.8255 (mpp) REVERT: B 3003 MET cc_start: 0.8722 (mtp) cc_final: 0.8456 (mtt) REVERT: B 3072 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8777 (mtt) REVERT: B 3147 TYR cc_start: 0.8261 (m-80) cc_final: 0.7961 (m-80) REVERT: B 3689 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: B 3819 MET cc_start: 0.7566 (mtt) cc_final: 0.7249 (mpp) REVERT: B 3854 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8933 (t80) REVERT: B 4161 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: B 4306 PHE cc_start: 0.7803 (m-80) cc_final: 0.7286 (m-80) REVERT: C 995 MET cc_start: 0.8681 (tpt) cc_final: 0.7993 (tpp) REVERT: C 2150 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7188 (mpp) REVERT: C 2685 TYR cc_start: 0.7722 (t80) cc_final: 0.7200 (t80) REVERT: C 2840 MET cc_start: 0.8703 (mmt) cc_final: 0.7806 (mmt) REVERT: C 2843 MET cc_start: 0.8875 (mtm) cc_final: 0.8419 (ptp) REVERT: C 2844 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: C 2858 MET cc_start: 0.8650 (mmp) cc_final: 0.8256 (mpp) REVERT: C 2860 LEU cc_start: 0.9161 (pp) cc_final: 0.8885 (tm) REVERT: C 3003 MET cc_start: 0.8687 (mtp) cc_final: 0.8442 (mtt) REVERT: C 3072 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8753 (mtt) REVERT: C 3147 TYR cc_start: 0.8227 (m-80) cc_final: 0.7934 (m-80) REVERT: C 3689 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: C 3819 MET cc_start: 0.7570 (mtt) cc_final: 0.7236 (mpp) REVERT: C 3854 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8931 (t80) REVERT: C 4161 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 4306 PHE cc_start: 0.7796 (m-80) cc_final: 0.7274 (m-80) REVERT: D 964 MET cc_start: 0.4280 (pmm) cc_final: 0.4078 (mpp) REVERT: D 995 MET cc_start: 0.8722 (tpt) cc_final: 0.8007 (tpp) REVERT: D 2150 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: D 2584 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8097 (mmt) REVERT: D 2685 TYR cc_start: 0.7418 (t80) cc_final: 0.7198 (t80) REVERT: D 2779 LEU cc_start: 0.9466 (mm) cc_final: 0.9232 (mt) REVERT: D 2840 MET cc_start: 0.8779 (mmt) cc_final: 0.7888 (mmt) REVERT: D 2843 MET cc_start: 0.8939 (mtm) cc_final: 0.8419 (ptp) REVERT: D 2844 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: D 2858 MET cc_start: 0.8666 (mmp) cc_final: 0.8282 (mpp) REVERT: D 3003 MET cc_start: 0.8673 (mtp) cc_final: 0.8427 (mtt) REVERT: D 3072 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: D 3147 TYR cc_start: 0.8243 (m-80) cc_final: 0.7938 (m-80) REVERT: D 3689 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7775 (mpp) REVERT: D 3819 MET cc_start: 0.7571 (mtt) cc_final: 0.7246 (mpp) REVERT: D 3854 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8934 (t80) REVERT: D 4161 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: D 4306 PHE cc_start: 0.7798 (m-80) cc_final: 0.7279 (m-80) outliers start: 97 outliers final: 36 residues processed: 819 average time/residue: 2.1930 time to fit residues: 2575.0827 Evaluate side-chains 814 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 757 time to evaluate : 12.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2844 MET Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2844 MET Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 20.0000 chunk 1504 optimal weight: 4.9990 chunk 330 optimal weight: 50.0000 chunk 980 optimal weight: 10.0000 chunk 412 optimal weight: 7.9990 chunk 1671 optimal weight: 0.9990 chunk 1387 optimal weight: 0.5980 chunk 774 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 553 optimal weight: 7.9990 chunk 877 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2802 ASN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 141620 Z= 0.313 Angle : 0.620 18.056 191348 Z= 0.312 Chirality : 0.041 0.350 20988 Planarity : 0.005 0.135 24588 Dihedral : 5.540 89.244 19024 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 0.55 % Allowed : 7.63 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.06), residues: 17212 helix: 1.95 (0.06), residues: 8988 sheet: -0.14 (0.12), residues: 1748 loop : -0.34 (0.07), residues: 6476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D2773 HIS 0.009 0.001 HIS B3732 PHE 0.025 0.002 PHE A2954 TYR 0.044 0.001 TYR C2801 ARG 0.018 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 772 time to evaluate : 12.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.8678 (tpt) cc_final: 0.7944 (tpp) REVERT: A 2685 TYR cc_start: 0.7633 (t80) cc_final: 0.7255 (t80) REVERT: A 2779 LEU cc_start: 0.9415 (mm) cc_final: 0.9191 (mt) REVERT: A 2843 MET cc_start: 0.8834 (mtm) cc_final: 0.8434 (ptm) REVERT: A 3003 MET cc_start: 0.8725 (mtp) cc_final: 0.8507 (mtt) REVERT: A 3072 MET cc_start: 0.9076 (mmm) cc_final: 0.8624 (mtp) REVERT: A 3147 TYR cc_start: 0.8291 (m-80) cc_final: 0.7997 (m-80) REVERT: A 3689 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: A 3819 MET cc_start: 0.7635 (mtt) cc_final: 0.7293 (mpp) REVERT: A 3854 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8936 (t80) REVERT: A 4161 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: A 4306 PHE cc_start: 0.7790 (m-80) cc_final: 0.7303 (m-80) REVERT: A 4748 MET cc_start: 0.7044 (mpt) cc_final: 0.6722 (mpt) REVERT: E 18 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8851 (mtmm) REVERT: G 50 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8253 (mtp85) REVERT: G 53 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9080 (mmtm) REVERT: B 981 MET cc_start: 0.7529 (ppp) cc_final: 0.7240 (pmm) REVERT: B 995 MET cc_start: 0.8699 (tpt) cc_final: 0.7939 (tpp) REVERT: B 2150 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: B 2685 TYR cc_start: 0.7676 (t80) cc_final: 0.7205 (t80) REVERT: B 2840 MET cc_start: 0.8691 (mmt) cc_final: 0.7910 (mmt) REVERT: B 2843 MET cc_start: 0.8857 (mtm) cc_final: 0.8427 (ptp) REVERT: B 3003 MET cc_start: 0.8715 (mtp) cc_final: 0.8484 (mtt) REVERT: B 3072 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8790 (mtt) REVERT: B 3147 TYR cc_start: 0.8248 (m-80) cc_final: 0.7950 (m-80) REVERT: B 3689 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: B 3819 MET cc_start: 0.7580 (mtt) cc_final: 0.7247 (mpp) REVERT: B 3854 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8936 (t80) REVERT: B 4161 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 4306 PHE cc_start: 0.7791 (m-80) cc_final: 0.7301 (m-80) REVERT: C 981 MET cc_start: 0.7485 (ppp) cc_final: 0.7200 (pmm) REVERT: C 995 MET cc_start: 0.8672 (tpt) cc_final: 0.7929 (tpp) REVERT: C 2150 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: C 2685 TYR cc_start: 0.7663 (t80) cc_final: 0.7210 (t80) REVERT: C 2779 LEU cc_start: 0.9425 (mm) cc_final: 0.9194 (mt) REVERT: C 2843 MET cc_start: 0.8803 (mtm) cc_final: 0.8464 (ptm) REVERT: C 3003 MET cc_start: 0.8710 (mtp) cc_final: 0.8478 (mtt) REVERT: C 3072 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8768 (mtt) REVERT: C 3147 TYR cc_start: 0.8232 (m-80) cc_final: 0.7936 (m-80) REVERT: C 3689 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7779 (mpp) REVERT: C 3819 MET cc_start: 0.7572 (mtt) cc_final: 0.7219 (mpp) REVERT: C 3854 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8935 (t80) REVERT: C 4161 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: D 349 MET cc_start: 0.8654 (mmt) cc_final: 0.8453 (mmt) REVERT: D 678 MET cc_start: 0.8572 (tpp) cc_final: 0.8022 (ttp) REVERT: D 995 MET cc_start: 0.8708 (tpt) cc_final: 0.7935 (tpp) REVERT: D 2150 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: D 2584 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8059 (mmt) REVERT: D 2685 TYR cc_start: 0.7629 (t80) cc_final: 0.7210 (t80) REVERT: D 2779 LEU cc_start: 0.9431 (mm) cc_final: 0.9204 (mt) REVERT: D 2843 MET cc_start: 0.8919 (mtm) cc_final: 0.8446 (ptm) REVERT: D 2860 LEU cc_start: 0.9183 (pp) cc_final: 0.8762 (tm) REVERT: D 3003 MET cc_start: 0.8675 (mtp) cc_final: 0.8467 (mtt) REVERT: D 3072 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: D 3147 TYR cc_start: 0.8247 (m-80) cc_final: 0.7945 (m-80) REVERT: D 3246 MET cc_start: 0.9158 (mtp) cc_final: 0.8918 (ptp) REVERT: D 3689 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7772 (mpp) REVERT: D 3819 MET cc_start: 0.7579 (mtt) cc_final: 0.7242 (mpp) REVERT: D 3854 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8937 (t80) REVERT: D 4161 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: D 4306 PHE cc_start: 0.7789 (m-80) cc_final: 0.7244 (m-80) outliers start: 84 outliers final: 45 residues processed: 812 average time/residue: 2.1454 time to fit residues: 2500.4972 Evaluate side-chains 816 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 752 time to evaluate : 10.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3090 VAL Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3246 MET Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3090 VAL Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2584 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3090 VAL Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 952 optimal weight: 10.0000 chunk 1220 optimal weight: 4.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 0.7980 chunk 933 optimal weight: 1.9990 chunk 1665 optimal weight: 6.9990 chunk 1042 optimal weight: 0.6980 chunk 1015 optimal weight: 0.5980 chunk 768 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4488 GLN ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 141620 Z= 0.173 Angle : 0.599 18.966 191348 Z= 0.297 Chirality : 0.040 0.371 20988 Planarity : 0.004 0.131 24588 Dihedral : 5.386 89.156 19024 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 0.55 % Allowed : 8.15 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.06), residues: 17212 helix: 2.03 (0.06), residues: 9008 sheet: -0.12 (0.12), residues: 1808 loop : -0.31 (0.08), residues: 6396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP D2773 HIS 0.009 0.001 HIS D3732 PHE 0.019 0.001 PHE A2954 TYR 0.046 0.001 TYR B2801 ARG 0.017 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 767 time to evaluate : 12.328 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 678 MET cc_start: 0.8533 (tpp) cc_final: 0.8156 (tpp) REVERT: A 981 MET cc_start: 0.7366 (ppp) cc_final: 0.7033 (pmm) REVERT: A 995 MET cc_start: 0.8649 (tpt) cc_final: 0.7888 (tpp) REVERT: A 2685 TYR cc_start: 0.7613 (t80) cc_final: 0.7204 (t80) REVERT: A 2779 LEU cc_start: 0.9376 (mm) cc_final: 0.9169 (mt) REVERT: A 2835 ARG cc_start: 0.8115 (mmp-170) cc_final: 0.7832 (mmp80) REVERT: A 2858 MET cc_start: 0.8694 (mmp) cc_final: 0.8320 (mpp) REVERT: A 3072 MET cc_start: 0.9085 (mmm) cc_final: 0.8583 (mtp) REVERT: A 3147 TYR cc_start: 0.8208 (m-80) cc_final: 0.7974 (m-80) REVERT: A 3819 MET cc_start: 0.7551 (mtt) cc_final: 0.7229 (mpp) REVERT: A 3854 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8753 (t80) REVERT: A 4161 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 4306 PHE cc_start: 0.7809 (m-80) cc_final: 0.7276 (m-80) REVERT: E 4 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6585 (tm-30) REVERT: E 18 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8854 (mtmm) REVERT: G 50 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8180 (mtp85) REVERT: G 53 LYS cc_start: 0.9311 (mmtm) cc_final: 0.9028 (mmtm) REVERT: B 678 MET cc_start: 0.8558 (tpp) cc_final: 0.8116 (ttp) REVERT: B 995 MET cc_start: 0.8695 (tpt) cc_final: 0.7913 (tpp) REVERT: B 2685 TYR cc_start: 0.7714 (t80) cc_final: 0.7264 (t80) REVERT: B 2840 MET cc_start: 0.8565 (mmt) cc_final: 0.7837 (mmt) REVERT: B 3003 MET cc_start: 0.8640 (mtp) cc_final: 0.8431 (mtt) REVERT: B 3072 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8835 (mtm) REVERT: B 3147 TYR cc_start: 0.8188 (m-80) cc_final: 0.7920 (m-80) REVERT: B 3689 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7674 (mpp) REVERT: B 3819 MET cc_start: 0.7447 (mtt) cc_final: 0.7134 (mpp) REVERT: B 3854 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8755 (t80) REVERT: B 4161 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 4306 PHE cc_start: 0.7754 (m-80) cc_final: 0.7238 (m-80) REVERT: C 678 MET cc_start: 0.8567 (tpp) cc_final: 0.8113 (ttp) REVERT: C 995 MET cc_start: 0.8659 (tpt) cc_final: 0.7859 (tpp) REVERT: C 2685 TYR cc_start: 0.7684 (t80) cc_final: 0.7215 (t80) REVERT: C 2779 LEU cc_start: 0.9418 (mm) cc_final: 0.9176 (mt) REVERT: C 2840 MET cc_start: 0.8752 (mmt) cc_final: 0.7997 (mmt) REVERT: C 2843 MET cc_start: 0.8785 (mtm) cc_final: 0.8582 (ptm) REVERT: C 2858 MET cc_start: 0.8647 (mmp) cc_final: 0.8289 (mpp) REVERT: C 3003 MET cc_start: 0.8646 (mtp) cc_final: 0.8437 (mtt) REVERT: C 3072 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8804 (mtm) REVERT: C 3147 TYR cc_start: 0.8171 (m-80) cc_final: 0.7916 (m-80) REVERT: C 3819 MET cc_start: 0.7431 (mtt) cc_final: 0.7112 (mpp) REVERT: C 3854 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8756 (t80) REVERT: C 4161 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: D 678 MET cc_start: 0.8536 (tpp) cc_final: 0.8172 (tpp) REVERT: D 995 MET cc_start: 0.8689 (tpt) cc_final: 0.7936 (tpp) REVERT: D 2685 TYR cc_start: 0.7592 (t80) cc_final: 0.7177 (t80) REVERT: D 2779 LEU cc_start: 0.9416 (mm) cc_final: 0.9156 (mt) REVERT: D 2840 MET cc_start: 0.8812 (mmt) cc_final: 0.8020 (mmt) REVERT: D 2843 MET cc_start: 0.8871 (mtm) cc_final: 0.8629 (ptm) REVERT: D 2858 MET cc_start: 0.8666 (mmp) cc_final: 0.8307 (mpp) REVERT: D 3003 MET cc_start: 0.8620 (mtp) cc_final: 0.8415 (mtt) REVERT: D 3072 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8818 (mtm) REVERT: D 3147 TYR cc_start: 0.8191 (m-80) cc_final: 0.7947 (m-80) REVERT: D 3819 MET cc_start: 0.7445 (mtt) cc_final: 0.7124 (mpp) REVERT: D 3854 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8759 (t80) REVERT: D 4161 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: D 4306 PHE cc_start: 0.7768 (m-80) cc_final: 0.7254 (m-80) outliers start: 83 outliers final: 38 residues processed: 814 average time/residue: 2.1342 time to fit residues: 2505.1808 Evaluate side-chains 802 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 752 time to evaluate : 12.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2777 GLU Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2927 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3090 VAL Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3090 VAL Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4161 GLU Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2689 MET Chi-restraints excluded: chain D residue 2927 GLN Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3090 VAL Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4161 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 8.9990 chunk 665 optimal weight: 8.9990 chunk 994 optimal weight: 9.9990 chunk 501 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 1058 optimal weight: 7.9990 chunk 1134 optimal weight: 30.0000 chunk 823 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 1309 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 141620 Z= 0.320 Angle : 0.628 21.171 191348 Z= 0.311 Chirality : 0.041 0.394 20988 Planarity : 0.005 0.130 24588 Dihedral : 5.387 89.827 19024 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.49 % Allowed : 8.43 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.06), residues: 17212 helix: 2.04 (0.06), residues: 8972 sheet: -0.06 (0.12), residues: 1692 loop : -0.33 (0.07), residues: 6548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP C2773 HIS 0.008 0.001 HIS D3732 PHE 0.025 0.002 PHE A2943 TYR 0.038 0.001 TYR C2801 ARG 0.020 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 762 time to evaluate : 12.224 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 678 MET cc_start: 0.8560 (tpp) cc_final: 0.8236 (tpp) REVERT: A 995 MET cc_start: 0.8662 (tpt) cc_final: 0.7905 (tpp) REVERT: A 2456 MET cc_start: 0.8847 (mmp) cc_final: 0.8625 (mmt) REVERT: A 2685 TYR cc_start: 0.7650 (t80) cc_final: 0.7293 (t80) REVERT: A 2779 LEU cc_start: 0.9437 (mm) cc_final: 0.9197 (mt) REVERT: A 2835 ARG cc_start: 0.8089 (mmp-170) cc_final: 0.7793 (mmp80) REVERT: A 2843 MET cc_start: 0.8824 (ptm) cc_final: 0.8612 (pmm) REVERT: A 2941 LEU cc_start: 0.9312 (pt) cc_final: 0.9106 (mm) REVERT: A 3072 MET cc_start: 0.9090 (mmm) cc_final: 0.8603 (mtp) REVERT: A 3147 TYR cc_start: 0.8259 (m-80) cc_final: 0.8015 (m-80) REVERT: A 3819 MET cc_start: 0.7561 (mtt) cc_final: 0.7217 (mpp) REVERT: A 3854 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8934 (t80) REVERT: A 4161 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: E 18 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8852 (mtmm) REVERT: F 4 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6709 (tm-30) REVERT: G 50 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8193 (mtp85) REVERT: G 53 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9034 (mmtm) REVERT: B 678 MET cc_start: 0.8578 (tpp) cc_final: 0.8284 (tpp) REVERT: B 995 MET cc_start: 0.8695 (tpt) cc_final: 0.7932 (tpp) REVERT: B 2456 MET cc_start: 0.8810 (mmp) cc_final: 0.8571 (mmt) REVERT: B 2685 TYR cc_start: 0.7722 (t80) cc_final: 0.7318 (t80) REVERT: B 2779 LEU cc_start: 0.9417 (mm) cc_final: 0.9158 (mt) REVERT: B 2828 MET cc_start: 0.8615 (mmm) cc_final: 0.8408 (tpt) REVERT: B 2840 MET cc_start: 0.8682 (mmt) cc_final: 0.7978 (mmt) REVERT: B 2843 MET cc_start: 0.8822 (ptm) cc_final: 0.8449 (pmm) REVERT: B 2858 MET cc_start: 0.8632 (mmp) cc_final: 0.8294 (mpp) REVERT: B 3003 MET cc_start: 0.8704 (mtp) cc_final: 0.8475 (mtt) REVERT: B 3072 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: B 3147 TYR cc_start: 0.8226 (m-80) cc_final: 0.7976 (m-80) REVERT: B 3689 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7775 (mpp) REVERT: B 3819 MET cc_start: 0.7500 (mtt) cc_final: 0.7170 (mpp) REVERT: B 3854 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8934 (t80) REVERT: B 4161 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: C 678 MET cc_start: 0.8591 (tpp) cc_final: 0.8285 (tpp) REVERT: C 995 MET cc_start: 0.8678 (tpt) cc_final: 0.7921 (tpp) REVERT: C 2456 MET cc_start: 0.8839 (mmp) cc_final: 0.8618 (mmt) REVERT: C 2685 TYR cc_start: 0.7713 (t80) cc_final: 0.7344 (t80) REVERT: C 2779 LEU cc_start: 0.9421 (mm) cc_final: 0.9163 (mt) REVERT: C 2843 MET cc_start: 0.8818 (mtm) cc_final: 0.8533 (ptm) REVERT: C 3003 MET cc_start: 0.8684 (mtp) cc_final: 0.8463 (mtt) REVERT: C 3072 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8785 (mtm) REVERT: C 3147 TYR cc_start: 0.8205 (m-80) cc_final: 0.7937 (m-80) REVERT: C 3819 MET cc_start: 0.7493 (mtt) cc_final: 0.7154 (mpp) REVERT: C 3854 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8935 (t80) REVERT: D 981 MET cc_start: 0.7411 (ppp) cc_final: 0.7108 (ppp) REVERT: D 995 MET cc_start: 0.8701 (tpt) cc_final: 0.7975 (tpp) REVERT: D 2456 MET cc_start: 0.8842 (mmp) cc_final: 0.8622 (mmt) REVERT: D 2685 TYR cc_start: 0.7573 (t80) cc_final: 0.7253 (t80) REVERT: D 2779 LEU cc_start: 0.9466 (mm) cc_final: 0.9218 (mt) REVERT: D 2840 MET cc_start: 0.8779 (mmt) cc_final: 0.7842 (mmt) REVERT: D 2843 MET cc_start: 0.8885 (mtm) cc_final: 0.8556 (ptm) REVERT: D 2858 MET cc_start: 0.8715 (mmp) cc_final: 0.8352 (mpp) REVERT: D 3003 MET cc_start: 0.8671 (mtp) cc_final: 0.8465 (mtt) REVERT: D 3072 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8807 (mtm) REVERT: D 3147 TYR cc_start: 0.8223 (m-80) cc_final: 0.7940 (m-80) REVERT: D 3233 HIS cc_start: 0.8367 (m-70) cc_final: 0.8085 (m90) REVERT: D 3819 MET cc_start: 0.7502 (mtt) cc_final: 0.7160 (mpp) REVERT: D 3854 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8939 (t80) outliers start: 74 outliers final: 43 residues processed: 805 average time/residue: 2.3125 time to fit residues: 2707.5463 Evaluate side-chains 813 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 760 time to evaluate : 11.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2927 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3090 VAL Chi-restraints excluded: chain B residue 3104 MET Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3090 VAL Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2927 GLN Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3090 VAL Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 3854 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 0.8980 chunk 1595 optimal weight: 20.0000 chunk 1455 optimal weight: 5.9990 chunk 1552 optimal weight: 4.9990 chunk 934 optimal weight: 2.9990 chunk 676 optimal weight: 7.9990 chunk 1218 optimal weight: 0.7980 chunk 476 optimal weight: 20.0000 chunk 1402 optimal weight: 10.0000 chunk 1467 optimal weight: 9.9990 chunk 1546 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2089 HIS ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2704 GLN A2890 GLN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4488 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4488 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 141620 Z= 0.191 Angle : 0.617 20.211 191348 Z= 0.302 Chirality : 0.040 0.420 20988 Planarity : 0.005 0.128 24588 Dihedral : 5.330 89.625 19024 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 0.53 % Allowed : 8.49 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.06), residues: 17212 helix: 2.09 (0.06), residues: 8964 sheet: -0.06 (0.12), residues: 1748 loop : -0.34 (0.08), residues: 6500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.001 TRP D2773 HIS 0.012 0.001 HIS D2550 PHE 0.018 0.001 PHE C4016 TYR 0.040 0.001 TYR C2801 ARG 0.018 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 763 time to evaluate : 11.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.8531 (tpp) cc_final: 0.8201 (tpp) REVERT: A 981 MET cc_start: 0.7393 (ppp) cc_final: 0.7111 (pmm) REVERT: A 995 MET cc_start: 0.8640 (tpt) cc_final: 0.7863 (tpp) REVERT: A 2456 MET cc_start: 0.8805 (mmp) cc_final: 0.8563 (mmt) REVERT: A 2685 TYR cc_start: 0.7600 (t80) cc_final: 0.7281 (t80) REVERT: A 2779 LEU cc_start: 0.9390 (mm) cc_final: 0.9149 (mt) REVERT: A 2858 MET cc_start: 0.8651 (mmp) cc_final: 0.8350 (mpp) REVERT: A 2988 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7648 (mmp80) REVERT: A 3022 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6840 (t80) REVERT: A 3038 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: A 3072 MET cc_start: 0.9087 (mmm) cc_final: 0.8595 (mtp) REVERT: A 3147 TYR cc_start: 0.8210 (m-80) cc_final: 0.8005 (m-80) REVERT: A 3819 MET cc_start: 0.7484 (mtt) cc_final: 0.7204 (mpp) REVERT: A 3854 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8794 (t80) REVERT: A 4161 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: E 18 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8842 (mtmm) REVERT: F 4 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6681 (tm-30) REVERT: G 50 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8136 (mtp85) REVERT: G 53 LYS cc_start: 0.9309 (mmtm) cc_final: 0.8997 (mmtm) REVERT: B 678 MET cc_start: 0.8548 (tpp) cc_final: 0.8263 (tpp) REVERT: B 995 MET cc_start: 0.8681 (tpt) cc_final: 0.7907 (tpp) REVERT: B 2456 MET cc_start: 0.8775 (mmp) cc_final: 0.8551 (mmt) REVERT: B 2685 TYR cc_start: 0.7708 (t80) cc_final: 0.7331 (t80) REVERT: B 2779 LEU cc_start: 0.9436 (mm) cc_final: 0.9206 (mt) REVERT: B 2840 MET cc_start: 0.8730 (mmt) cc_final: 0.8345 (mmt) REVERT: B 2858 MET cc_start: 0.8644 (mmp) cc_final: 0.8292 (mpp) REVERT: B 3003 MET cc_start: 0.8653 (mtp) cc_final: 0.8451 (mtt) REVERT: B 3022 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 3038 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: B 3072 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8838 (mtm) REVERT: B 3147 TYR cc_start: 0.8184 (m-80) cc_final: 0.7977 (m-80) REVERT: B 3689 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: B 3819 MET cc_start: 0.7402 (mtt) cc_final: 0.7156 (mpp) REVERT: B 3854 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8782 (t80) REVERT: B 4161 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 678 MET cc_start: 0.8567 (tpp) cc_final: 0.8139 (ttp) REVERT: C 995 MET cc_start: 0.8656 (tpt) cc_final: 0.7868 (tpp) REVERT: C 2456 MET cc_start: 0.8791 (mmp) cc_final: 0.8588 (mmt) REVERT: C 2685 TYR cc_start: 0.7671 (t80) cc_final: 0.7310 (t80) REVERT: C 2779 LEU cc_start: 0.9431 (mm) cc_final: 0.9186 (mt) REVERT: C 2843 MET cc_start: 0.8786 (mtm) cc_final: 0.8582 (ptm) REVERT: C 2858 MET cc_start: 0.8620 (mmp) cc_final: 0.8285 (mpp) REVERT: C 3003 MET cc_start: 0.8656 (mtp) cc_final: 0.8449 (mtt) REVERT: C 3022 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6828 (t80) REVERT: C 3038 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: C 3072 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: C 3147 TYR cc_start: 0.8172 (m-80) cc_final: 0.7946 (m-80) REVERT: C 3819 MET cc_start: 0.7409 (mtt) cc_final: 0.7147 (mpp) REVERT: C 3854 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8785 (t80) REVERT: C 3954 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8247 (mtm) REVERT: D 678 MET cc_start: 0.8518 (tpp) cc_final: 0.8073 (ttp) REVERT: D 981 MET cc_start: 0.7365 (ppp) cc_final: 0.7095 (ppp) REVERT: D 995 MET cc_start: 0.8678 (tpt) cc_final: 0.7916 (tpp) REVERT: D 2685 TYR cc_start: 0.7558 (t80) cc_final: 0.7208 (t80) REVERT: D 2779 LEU cc_start: 0.9432 (mm) cc_final: 0.9176 (mt) REVERT: D 2840 MET cc_start: 0.8752 (mmt) cc_final: 0.7841 (mmt) REVERT: D 2843 MET cc_start: 0.8869 (mtm) cc_final: 0.8645 (ptm) REVERT: D 3003 MET cc_start: 0.8643 (mtp) cc_final: 0.8437 (mtt) REVERT: D 3022 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6823 (t80) REVERT: D 3038 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: D 3072 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8836 (mtm) REVERT: D 3147 TYR cc_start: 0.8177 (m-80) cc_final: 0.7950 (m-80) REVERT: D 3819 MET cc_start: 0.7421 (mtt) cc_final: 0.7160 (mpp) REVERT: D 3854 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8795 (t80) outliers start: 80 outliers final: 46 residues processed: 811 average time/residue: 2.0652 time to fit residues: 2401.6483 Evaluate side-chains 822 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 757 time to evaluate : 12.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 3022 PHE Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2927 GLN Chi-restraints excluded: chain B residue 3022 PHE Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3090 VAL Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1948 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 3022 PHE Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3090 VAL Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 1948 MET Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2927 GLN Chi-restraints excluded: chain D residue 3022 PHE Chi-restraints excluded: chain D residue 3038 GLN Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3090 VAL Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 3854 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 0.5980 chunk 1641 optimal weight: 0.7980 chunk 1001 optimal weight: 5.9990 chunk 778 optimal weight: 8.9990 chunk 1140 optimal weight: 9.9990 chunk 1721 optimal weight: 6.9990 chunk 1584 optimal weight: 10.0000 chunk 1370 optimal weight: 0.2980 chunk 142 optimal weight: 5.9990 chunk 1058 optimal weight: 8.9990 chunk 840 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2089 HIS ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2089 HIS ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 141620 Z= 0.223 Angle : 0.632 20.273 191348 Z= 0.308 Chirality : 0.040 0.418 20988 Planarity : 0.005 0.127 24588 Dihedral : 5.306 89.390 19024 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.45 % Allowed : 8.69 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.43 (0.06), residues: 17212 helix: 2.09 (0.06), residues: 8964 sheet: -0.05 (0.12), residues: 1748 loop : -0.34 (0.08), residues: 6500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.001 TRP D2773 HIS 0.013 0.001 HIS C2550 PHE 0.025 0.001 PHE A2943 TYR 0.041 0.001 TYR C2801 ARG 0.021 0.000 ARG D2835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 762 time to evaluate : 12.873 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 678 MET cc_start: 0.8513 (tpp) cc_final: 0.8200 (tpp) REVERT: A 895 MET cc_start: 0.9108 (mpm) cc_final: 0.8891 (mmm) REVERT: A 981 MET cc_start: 0.7443 (ppp) cc_final: 0.7098 (pmm) REVERT: A 995 MET cc_start: 0.8640 (tpt) cc_final: 0.7931 (tpp) REVERT: A 2688 MET cc_start: 0.7116 (mpm) cc_final: 0.6398 (tmm) REVERT: A 2779 LEU cc_start: 0.9404 (mm) cc_final: 0.9185 (mt) REVERT: A 2843 MET cc_start: 0.8886 (ptm) cc_final: 0.8589 (pmt) REVERT: A 2858 MET cc_start: 0.8643 (mmp) cc_final: 0.8316 (mpp) REVERT: A 2988 ARG cc_start: 0.7900 (mmp80) cc_final: 0.7665 (mmp80) REVERT: A 3038 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: A 3072 MET cc_start: 0.9087 (mmm) cc_final: 0.8600 (mtp) REVERT: A 3819 MET cc_start: 0.7459 (mtt) cc_final: 0.7213 (mpp) REVERT: A 3854 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8819 (t80) REVERT: A 3954 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8228 (mtm) REVERT: A 4161 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: E 18 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8844 (mtmm) REVERT: F 4 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6712 (tm-30) REVERT: G 50 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8143 (mtp85) REVERT: G 53 LYS cc_start: 0.9305 (mmtm) cc_final: 0.8991 (mmtm) REVERT: B 678 MET cc_start: 0.8548 (tpp) cc_final: 0.8109 (ttp) REVERT: B 895 MET cc_start: 0.9091 (mpm) cc_final: 0.8860 (mmm) REVERT: B 964 MET cc_start: 0.3844 (mpt) cc_final: 0.3638 (mpt) REVERT: B 981 MET cc_start: 0.7375 (ppp) cc_final: 0.6975 (ppp) REVERT: B 995 MET cc_start: 0.8684 (tpt) cc_final: 0.7902 (tpp) REVERT: B 2192 MET cc_start: 0.8538 (tpp) cc_final: 0.8145 (tpp) REVERT: B 2456 MET cc_start: 0.8789 (mmp) cc_final: 0.8574 (mmt) REVERT: B 2685 TYR cc_start: 0.7662 (t80) cc_final: 0.7294 (t80) REVERT: B 2779 LEU cc_start: 0.9431 (mm) cc_final: 0.9215 (mt) REVERT: B 2840 MET cc_start: 0.8711 (mmt) cc_final: 0.8317 (mmt) REVERT: B 2858 MET cc_start: 0.8659 (mmp) cc_final: 0.8299 (mpp) REVERT: B 3003 MET cc_start: 0.8667 (mtp) cc_final: 0.8464 (mtt) REVERT: B 3022 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 3038 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: B 3072 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8837 (mtm) REVERT: B 3689 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7721 (mpp) REVERT: B 3819 MET cc_start: 0.7424 (mtt) cc_final: 0.7192 (mpp) REVERT: B 3854 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8809 (t80) REVERT: B 4161 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: C 678 MET cc_start: 0.8564 (tpp) cc_final: 0.8119 (ttp) REVERT: C 964 MET cc_start: 0.3756 (mpt) cc_final: 0.3547 (mpt) REVERT: C 981 MET cc_start: 0.7326 (ppp) cc_final: 0.6933 (ppp) REVERT: C 995 MET cc_start: 0.8658 (tpt) cc_final: 0.7868 (tpp) REVERT: C 2688 MET cc_start: 0.7231 (mpm) cc_final: 0.6190 (tmm) REVERT: C 2779 LEU cc_start: 0.9425 (mm) cc_final: 0.9186 (mt) REVERT: C 2843 MET cc_start: 0.8792 (mtm) cc_final: 0.8545 (ptp) REVERT: C 2858 MET cc_start: 0.8654 (mmp) cc_final: 0.8314 (mpp) REVERT: C 3003 MET cc_start: 0.8656 (mtp) cc_final: 0.8452 (mtt) REVERT: C 3022 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6836 (t80) REVERT: C 3038 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: C 3072 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8805 (mtm) REVERT: C 3147 TYR cc_start: 0.8169 (m-80) cc_final: 0.7961 (m-80) REVERT: C 3819 MET cc_start: 0.7409 (mtt) cc_final: 0.7169 (mpp) REVERT: C 3854 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8811 (t80) REVERT: C 3954 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: D 678 MET cc_start: 0.8519 (tpp) cc_final: 0.8209 (tpp) REVERT: D 981 MET cc_start: 0.7376 (ppp) cc_final: 0.7176 (pmm) REVERT: D 995 MET cc_start: 0.8688 (tpt) cc_final: 0.7924 (tpp) REVERT: D 2688 MET cc_start: 0.7148 (mpm) cc_final: 0.6321 (tmm) REVERT: D 2695 MET cc_start: 0.8522 (mmm) cc_final: 0.8262 (mpm) REVERT: D 2779 LEU cc_start: 0.9427 (mm) cc_final: 0.9174 (mt) REVERT: D 2843 MET cc_start: 0.8895 (mtm) cc_final: 0.8513 (ptp) REVERT: D 2858 MET cc_start: 0.8674 (mmp) cc_final: 0.8372 (mpp) REVERT: D 3003 MET cc_start: 0.8651 (mtp) cc_final: 0.8442 (mtt) REVERT: D 3022 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6820 (t80) REVERT: D 3038 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: D 3072 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: D 3147 TYR cc_start: 0.8194 (m-80) cc_final: 0.7965 (m-80) REVERT: D 3819 MET cc_start: 0.7422 (mtt) cc_final: 0.7164 (mpp) REVERT: D 3854 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8817 (t80) outliers start: 68 outliers final: 44 residues processed: 800 average time/residue: 2.1402 time to fit residues: 2452.6878 Evaluate side-chains 819 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 756 time to evaluate : 12.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3216 GLU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3322 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3954 MET Chi-restraints excluded: chain A residue 4161 GLU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1727 VAL Chi-restraints excluded: chain B residue 2142 MET Chi-restraints excluded: chain B residue 2150 MET Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2927 GLN Chi-restraints excluded: chain B residue 3022 PHE Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3090 VAL Chi-restraints excluded: chain B residue 3104 MET Chi-restraints excluded: chain B residue 3216 GLU Chi-restraints excluded: chain B residue 3217 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4161 GLU Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2150 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2927 GLN Chi-restraints excluded: chain C residue 3022 PHE Chi-restraints excluded: chain C residue 3038 GLN Chi-restraints excluded: chain C residue 3072 MET Chi-restraints excluded: chain C residue 3090 VAL Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3216 GLU Chi-restraints excluded: chain C residue 3217 GLU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3954 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1727 VAL Chi-restraints excluded: chain D residue 2142 MET Chi-restraints excluded: chain D residue 2150 MET Chi-restraints excluded: chain D residue 2927 GLN Chi-restraints excluded: chain D residue 3022 PHE Chi-restraints excluded: chain D residue 3038 GLN Chi-restraints excluded: chain D residue 3072 MET Chi-restraints excluded: chain D residue 3090 VAL Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3216 GLU Chi-restraints excluded: chain D residue 3217 GLU Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 3854 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 0.5980 chunk 1460 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 1264 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 1373 optimal weight: 3.9990 chunk 574 optimal weight: 9.9990 chunk 1409 optimal weight: 0.0040 chunk 173 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 overall best weight: 3.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS ** D 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2890 GLN ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.040980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.030376 restraints weight = 1384048.580| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.91 r_work: 0.2870 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 141620 Z= 0.240 Angle : 0.634 20.308 191348 Z= 0.310 Chirality : 0.040 0.419 20988 Planarity : 0.004 0.126 24588 Dihedral : 5.302 88.283 19024 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 0.50 % Allowed : 8.77 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.06), residues: 17212 helix: 2.11 (0.06), residues: 8948 sheet: -0.02 (0.12), residues: 1732 loop : -0.34 (0.08), residues: 6532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.001 TRP D2773 HIS 0.012 0.001 HIS B 395 PHE 0.025 0.001 PHE C2954 TYR 0.055 0.001 TYR B2801 ARG 0.021 0.000 ARG C2835 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41170.23 seconds wall clock time: 717 minutes 40.17 seconds (43060.17 seconds total)