Starting phenix.real_space_refine on Tue Mar 19 02:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq3_42459/03_2024/8uq3_42459_updated.pdb" } resolution = 3.18 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= 0.009 sd= 0.026 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 940 5.16 5 C 88280 2.51 5 N 23600 2.21 5 O 25852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A ASP 1167": "OD1" <-> "OD2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A ASP 1274": "OD1" <-> "OD2" Residue "A ASP 1785": "OD1" <-> "OD2" Residue "A PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2511": "OD1" <-> "OD2" Residue "A PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2885": "OD1" <-> "OD2" Residue "A PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A GLU 3069": "OE1" <-> "OE2" Residue "A PHE 3117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3192": "NH1" <-> "NH2" Residue "A PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4030": "OD1" <-> "OD2" Residue "A PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4964": "OD1" <-> "OD2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H ASP 12": "OD1" <-> "OD2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 910": "OD1" <-> "OD2" Residue "B ASP 1167": "OD1" <-> "OD2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1199": "OD1" <-> "OD2" Residue "B ASP 1274": "OD1" <-> "OD2" Residue "B ASP 1785": "OD1" <-> "OD2" Residue "B PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2511": "OD1" <-> "OD2" Residue "B PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2885": "OD1" <-> "OD2" Residue "B PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B GLU 3069": "OE1" <-> "OE2" Residue "B PHE 3117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3192": "NH1" <-> "NH2" Residue "B PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4030": "OD1" <-> "OD2" Residue "B PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4964": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 910": "OD1" <-> "OD2" Residue "C ASP 1167": "OD1" <-> "OD2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1199": "OD1" <-> "OD2" Residue "C ASP 1274": "OD1" <-> "OD2" Residue "C ASP 1785": "OD1" <-> "OD2" Residue "C PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2511": "OD1" <-> "OD2" Residue "C PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2885": "OD1" <-> "OD2" Residue "C PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C GLU 3069": "OE1" <-> "OE2" Residue "C PHE 3117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3192": "NH1" <-> "NH2" Residue "C PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4030": "OD1" <-> "OD2" Residue "C PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4964": "OD1" <-> "OD2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 910": "OD1" <-> "OD2" Residue "D ASP 1167": "OD1" <-> "OD2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1199": "OD1" <-> "OD2" Residue "D ASP 1274": "OD1" <-> "OD2" Residue "D ASP 1785": "OD1" <-> "OD2" Residue "D PHE 1942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2511": "OD1" <-> "OD2" Residue "D PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2885": "OD1" <-> "OD2" Residue "D PHE 2907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D GLU 3069": "OE1" <-> "OE2" Residue "D PHE 3117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3192": "NH1" <-> "NH2" Residue "D PHE 3319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4030": "OD1" <-> "OD2" Residue "D PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4964": "OD1" <-> "OD2" Time to flip residues: 0.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138700 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33092 SG CYS A4888 176.710 176.210 88.711 1.00 84.89 S ATOM 33117 SG CYS A4891 176.658 178.625 91.619 1.00 82.16 S ATOM 70135 SG CYS B4888 202.300 176.688 88.728 1.00 84.89 S ATOM 70160 SG CYS B4891 199.886 176.637 91.637 1.00 82.16 S ATOM A030I SG CYS C4888 201.765 202.305 88.711 1.00 84.89 S ATOM A0317 SG CYS C4891 201.818 199.893 91.621 1.00 82.16 S ATOM A0T2L SG CYS D4888 176.156 201.769 88.714 1.00 84.89 S ATOM A0T3A SG CYS D4891 178.570 201.822 91.623 1.00 82.16 S Time building chain proxies: 93.75, per 1000 atoms: 0.68 Number of scatterers: 138700 At special positions: 0 Unit cell: (379.31, 379.31, 214.97, 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 940 16.00 P 24 15.00 O 25852 8.00 N 23600 7.00 C 88280 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 40.05 Conformation dependent library (CDL) restraints added in 33.3 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: 668 helices and 76 sheets defined 59.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 37.87 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.026A 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 253 through 259 removed outlier: 3.833A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 6.202A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.936A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.599A 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 523 through 542 removed outlier: 4.638A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.696A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.128A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.803A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 590' Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.752A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.150A 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: 4.545A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.507A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.012A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.537A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 5.192A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1040 through 1061 removed outlier: 4.008A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.979A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 7.033A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.911A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.871A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.289A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.799A 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: 3.704A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.781A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.994A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.568A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 removed outlier: 3.542A pdb=" N LYS A1788 " --> pdb=" O LEU A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.204A pdb=" N LEU A1839 " --> pdb=" O HIS A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 4.471A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1955 removed outlier: 4.143A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1934 " --> pdb=" O ASP A1930 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A1952 " --> pdb=" O MET A1948 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1967 removed outlier: 4.447A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.671A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.626A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.639A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.769A 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: 3.944A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.600A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2183 removed outlier: 5.096A pdb=" N MET A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N HIS A2168 " --> pdb=" O ALA A2164 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.611A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.222A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.672A 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: 3.670A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2412 Proline residue: A2404 - end of helix removed outlier: 9.019A pdb=" N HIS A2407 " --> pdb=" O ALA A2403 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2455 through 2460 removed outlier: 3.668A pdb=" N GLY A2459 " --> pdb=" O ASP A2455 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE A2460 " --> pdb=" O MET A2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2455 through 2460' Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.947A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2504 removed outlier: 5.084A pdb=" N LEU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) Proline residue: A2494 - end of helix removed outlier: 4.750A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2532 removed outlier: 5.183A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2558 removed outlier: 3.597A pdb=" N ILE A2545 " --> pdb=" O HIS A2541 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.265A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2618 Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 removed outlier: 3.778A pdb=" N LEU A2666 " --> pdb=" O PHE A2662 " (cutoff:3.500A) Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2697 removed outlier: 5.156A pdb=" N SER A2697 " --> pdb=" O SER A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2716 through 2740 removed outlier: 4.438A pdb=" N PHE A2720 " --> pdb=" O LYS A2716 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A2723 " --> pdb=" O TYR A2719 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A2724 " --> pdb=" O PHE A2720 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU A2726 " --> pdb=" O ASN A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.206A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 5.059A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TRP A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 4.445A pdb=" N GLY A2786 " --> pdb=" O MET A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 3.980A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.273A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.515A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2948 removed outlier: 3.566A pdb=" N SER A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.850A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.985A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 4.314A pdb=" N GLN A3079 " --> pdb=" O LEU A3075 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.208A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3125 through 3143 Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 3.979A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 removed outlier: 3.671A pdb=" N GLY A3164 " --> pdb=" O ALA A3160 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3188 removed outlier: 3.793A pdb=" N SER A3188 " --> pdb=" O TYR A3184 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.903A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.961A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3253 removed outlier: 5.232A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 5.091A pdb=" N GLU A3251 " --> pdb=" O SER A3247 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A3252 " --> pdb=" O ARG A3248 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 3.914A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A3300 " --> pdb=" O MET A3296 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.966A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3329 removed outlier: 5.000A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 4.420A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 3.640A pdb=" N MET A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.667A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.265A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 3.623A pdb=" N GLU A3642 " --> pdb=" O ASP A3638 " (cutoff:3.500A) Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.879A 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 removed outlier: 3.889A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.976A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.886A 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: 4.674A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.690A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 4.148A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.650A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.651A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.513A pdb=" N PHE A4020 " --> pdb=" O PHE A4016 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.609A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.106A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.256A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.718A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.540A 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 4184 through 4208 removed outlier: 5.267A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4271 removed outlier: 3.662A pdb=" N LEU A4255 " --> pdb=" O ASN A4251 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A4260 " --> pdb=" O MET A4256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER A4263 " --> pdb=" O LEU A4259 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS A4265 " --> pdb=" O LEU A4261 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A4269 " --> pdb=" O LYS A4265 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.836A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.033A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 4.240A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.425A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.471A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 3.846A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4701 removed outlier: 3.891A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.865A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.705A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.902A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.164A 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: 4.375A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.908A 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: 4.059A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.338A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.984A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.968A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 4.785A pdb=" N ILE A3180 " --> pdb=" O LYS A3177 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 4.960A pdb=" N ILE A2382 " --> pdb=" O GLU A2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.026A 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 253 through 259 removed outlier: 3.832A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 removed outlier: 6.203A pdb=" N SER B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.936A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.599A 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 523 through 542 removed outlier: 4.638A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.697A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.128A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.803A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 590' Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.752A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.149A 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: 4.545A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.507A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 875 through 901 removed outlier: 4.013A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.537A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 removed outlier: 5.192A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1040 through 1061 removed outlier: 4.009A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.979A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 7.033A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.911A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1494 Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.872A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.289A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.798A 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: 3.705A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.782A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.994A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.568A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1802 removed outlier: 3.542A pdb=" N LYS B1788 " --> pdb=" O LEU B1784 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 removed outlier: 4.204A pdb=" N LEU B1839 " --> pdb=" O HIS B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 4.472A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1955 removed outlier: 4.143A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B1934 " --> pdb=" O ASP B1930 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN B1952 " --> pdb=" O MET B1948 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET B1953 " --> pdb=" O GLN B1949 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1967 removed outlier: 4.448A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.670A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.626A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.638A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.769A 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: 3.944A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.601A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2183 removed outlier: 5.097A pdb=" N MET B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N HIS B2168 " --> pdb=" O ALA B2164 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.611A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.222A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.671A 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: 3.670A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B2320 " --> pdb=" O ASN B2316 " (cutoff:3.500A) Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2412 Proline residue: B2404 - end of helix removed outlier: 9.019A pdb=" N HIS B2407 " --> pdb=" O ALA B2403 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B2408 " --> pdb=" O PRO B2404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B2409 " --> pdb=" O GLU B2405 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2455 through 2460 removed outlier: 3.668A pdb=" N GLY B2459 " --> pdb=" O ASP B2455 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE B2460 " --> pdb=" O MET B2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2455 through 2460' Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.947A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2504 removed outlier: 5.084A pdb=" N LEU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) Proline residue: B2494 - end of helix removed outlier: 4.749A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2510 through 2532 removed outlier: 5.182A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2558 removed outlier: 3.598A pdb=" N ILE B2545 " --> pdb=" O HIS B2541 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.265A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2603 through 2618 Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 removed outlier: 3.779A pdb=" N LEU B2666 " --> pdb=" O PHE B2662 " (cutoff:3.500A) Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2697 removed outlier: 5.156A pdb=" N SER B2697 " --> pdb=" O SER B2693 " (cutoff:3.500A) Processing helix chain 'B' and resid 2716 through 2740 removed outlier: 4.438A pdb=" N PHE B2720 " --> pdb=" O LYS B2716 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS B2723 " --> pdb=" O TYR B2719 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B2724 " --> pdb=" O PHE B2720 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B2726 " --> pdb=" O ASN B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.207A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 5.058A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP B2773 " --> pdb=" O GLU B2769 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 4.445A pdb=" N GLY B2786 " --> pdb=" O MET B2782 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 3.980A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.273A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.515A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2948 removed outlier: 3.566A pdb=" N SER B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.851A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.985A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 4.315A pdb=" N GLN B3079 " --> pdb=" O LEU B3075 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.208A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3125 through 3143 Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 3.978A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 removed outlier: 3.671A pdb=" N GLY B3164 " --> pdb=" O ALA B3160 " (cutoff:3.500A) Processing helix chain 'B' and resid 3182 through 3188 removed outlier: 3.794A pdb=" N SER B3188 " --> pdb=" O TYR B3184 " (cutoff:3.500A) Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.903A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.960A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3253 removed outlier: 5.233A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 5.090A pdb=" N GLU B3251 " --> pdb=" O SER B3247 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS B3252 " --> pdb=" O ARG B3248 " (cutoff:3.500A) Processing helix chain 'B' and resid 3269 through 3288 Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 3.914A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B3300 " --> pdb=" O MET B3296 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL B3301 " --> pdb=" O LYS B3297 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.965A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3329 removed outlier: 5.000A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 4.420A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 3.640A pdb=" N MET B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.667A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.264A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 3.622A pdb=" N GLU B3642 " --> pdb=" O ASP B3638 " (cutoff:3.500A) Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.880A 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 removed outlier: 3.889A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.976A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.887A 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: 4.674A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.691A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 4.148A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.651A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.651A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.512A pdb=" N PHE B4020 " --> pdb=" O PHE B4016 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.608A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.106A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.257A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.718A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.541A 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 4184 through 4208 removed outlier: 5.267A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4271 removed outlier: 3.662A pdb=" N LEU B4255 " --> pdb=" O ASN B4251 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B4260 " --> pdb=" O MET B4256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B4261 " --> pdb=" O ARG B4257 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER B4263 " --> pdb=" O LEU B4259 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS B4265 " --> pdb=" O LEU B4261 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B4269 " --> pdb=" O LYS B4265 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.835A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.033A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 4.240A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.425A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.471A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 3.846A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4701 removed outlier: 3.890A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.865A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.705A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.901A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.164A 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: 4.375A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.908A 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: 4.059A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.338A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.984A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.969A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 4.785A pdb=" N ILE B3180 " --> pdb=" O LYS B3177 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 4.960A pdb=" N ILE B2382 " --> pdb=" O GLU B2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.026A 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 253 through 259 removed outlier: 3.832A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 removed outlier: 6.202A pdb=" N SER C 268 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.936A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.600A 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 523 through 542 removed outlier: 4.637A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 3.696A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.128A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.803A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 590' Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.751A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.149A 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: 4.545A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.506A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 875 through 901 removed outlier: 4.012A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.537A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 961 removed outlier: 5.192A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1040 through 1061 removed outlier: 4.009A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.979A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 7.033A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.911A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1494 Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.871A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.289A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.798A 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: 3.705A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.781A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.994A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.567A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 removed outlier: 3.543A pdb=" N LYS C1788 " --> pdb=" O LEU C1784 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 removed outlier: 4.204A pdb=" N LEU C1839 " --> pdb=" O HIS C1835 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 4.471A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) Processing helix chain 'C' and resid 1899 through 1955 removed outlier: 4.144A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C1934 " --> pdb=" O ASP C1930 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN C1952 " --> pdb=" O MET C1948 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET C1953 " --> pdb=" O GLN C1949 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1967 removed outlier: 4.447A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.671A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.626A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.639A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.769A 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: 3.944A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.600A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2183 removed outlier: 5.096A pdb=" N MET C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N HIS C2168 " --> pdb=" O ALA C2164 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.611A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.222A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.672A 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: 3.670A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 removed outlier: 3.680A pdb=" N VAL C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C2320 " --> pdb=" O ASN C2316 " (cutoff:3.500A) Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2412 Proline residue: C2404 - end of helix removed outlier: 9.018A pdb=" N HIS C2407 " --> pdb=" O ALA C2403 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C2408 " --> pdb=" O PRO C2404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C2409 " --> pdb=" O GLU C2405 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2455 through 2460 removed outlier: 3.668A pdb=" N GLY C2459 " --> pdb=" O ASP C2455 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE C2460 " --> pdb=" O MET C2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2455 through 2460' Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.946A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2504 removed outlier: 5.083A pdb=" N LEU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) Proline residue: C2494 - end of helix removed outlier: 4.751A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2510 through 2532 removed outlier: 5.183A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2558 removed outlier: 3.597A pdb=" N ILE C2545 " --> pdb=" O HIS C2541 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.265A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2603 through 2618 Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.155A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 removed outlier: 3.778A pdb=" N LEU C2666 " --> pdb=" O PHE C2662 " (cutoff:3.500A) Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2697 removed outlier: 5.156A pdb=" N SER C2697 " --> pdb=" O SER C2693 " (cutoff:3.500A) Processing helix chain 'C' and resid 2716 through 2740 removed outlier: 4.438A pdb=" N PHE C2720 " --> pdb=" O LYS C2716 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS C2723 " --> pdb=" O TYR C2719 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C2724 " --> pdb=" O PHE C2720 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU C2726 " --> pdb=" O ASN C2722 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.205A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 5.058A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TRP C2773 " --> pdb=" O GLU C2769 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 4.445A pdb=" N GLY C2786 " --> pdb=" O MET C2782 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 3.980A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.272A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.514A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2948 removed outlier: 3.566A pdb=" N SER C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.850A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.984A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 4.315A pdb=" N GLN C3079 " --> pdb=" O LEU C3075 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.208A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3125 through 3143 Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 3.979A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 removed outlier: 3.671A pdb=" N GLY C3164 " --> pdb=" O ALA C3160 " (cutoff:3.500A) Processing helix chain 'C' and resid 3182 through 3188 removed outlier: 3.793A pdb=" N SER C3188 " --> pdb=" O TYR C3184 " (cutoff:3.500A) Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.903A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.961A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3253 removed outlier: 5.232A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 5.091A pdb=" N GLU C3251 " --> pdb=" O SER C3247 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS C3252 " --> pdb=" O ARG C3248 " (cutoff:3.500A) Processing helix chain 'C' and resid 3269 through 3288 Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 3.914A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C3300 " --> pdb=" O MET C3296 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C3301 " --> pdb=" O LYS C3297 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.965A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3329 removed outlier: 5.000A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 4.420A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 3.640A pdb=" N MET C3605 " --> pdb=" O ALA C3601 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.667A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.264A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 3.623A pdb=" N GLU C3642 " --> pdb=" O ASP C3638 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.880A 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 removed outlier: 3.890A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.975A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.886A 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: 4.674A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.690A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 4.148A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.650A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.652A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.512A pdb=" N PHE C4020 " --> pdb=" O PHE C4016 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.608A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.106A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.256A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.718A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.541A 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 4184 through 4208 removed outlier: 5.267A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4271 removed outlier: 3.662A pdb=" N LEU C4255 " --> pdb=" O ASN C4251 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C4260 " --> pdb=" O MET C4256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C4261 " --> pdb=" O ARG C4257 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C4263 " --> pdb=" O LEU C4259 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C4264 " --> pdb=" O SER C4260 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS C4265 " --> pdb=" O LEU C4261 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C4269 " --> pdb=" O LYS C4265 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.835A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.033A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 4.241A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.425A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.471A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 3.846A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4701 removed outlier: 3.891A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.865A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.705A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.902A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.164A 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: 4.375A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.908A 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: 4.059A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.338A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.984A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.968A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 4.785A pdb=" N ILE C3180 " --> pdb=" O LYS C3177 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 4.961A pdb=" N ILE C2382 " --> pdb=" O GLU C2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.026A 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 253 through 259 removed outlier: 3.832A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 6.202A pdb=" N SER D 268 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.935A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 4.599A 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 523 through 542 removed outlier: 4.638A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 3.696A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.129A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.802A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 590' Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.752A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.150A 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: 4.545A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.507A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 875 through 901 removed outlier: 4.012A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 3.537A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 961 removed outlier: 5.192A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1040 through 1061 removed outlier: 4.008A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.978A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 7.033A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.911A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1494 Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.871A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.289A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.799A 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: 3.704A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.781A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.993A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.568A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1802 removed outlier: 3.542A pdb=" N LYS D1788 " --> pdb=" O LEU D1784 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.203A pdb=" N LEU D1839 " --> pdb=" O HIS D1835 " (cutoff:3.500A) Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 4.471A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) Processing helix chain 'D' and resid 1899 through 1955 removed outlier: 4.144A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D1934 " --> pdb=" O ASP D1930 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN D1952 " --> pdb=" O MET D1948 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET D1953 " --> pdb=" O GLN D1949 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1967 removed outlier: 4.447A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.671A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.627A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.639A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.770A 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: 3.945A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.600A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2183 removed outlier: 5.097A pdb=" N MET D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N HIS D2168 " --> pdb=" O ALA D2164 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.611A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.223A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.671A 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: 3.670A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 removed outlier: 3.681A pdb=" N VAL D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D2320 " --> pdb=" O ASN D2316 " (cutoff:3.500A) Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2412 Proline residue: D2404 - end of helix removed outlier: 9.018A pdb=" N HIS D2407 " --> pdb=" O ALA D2403 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D2408 " --> pdb=" O PRO D2404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D2409 " --> pdb=" O GLU D2405 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2455 through 2460 removed outlier: 3.668A pdb=" N GLY D2459 " --> pdb=" O ASP D2455 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE D2460 " --> pdb=" O MET D2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2455 through 2460' Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.947A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2504 removed outlier: 5.084A pdb=" N LEU D2493 " --> pdb=" O GLU D2489 " (cutoff:3.500A) Proline residue: D2494 - end of helix removed outlier: 4.751A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2510 through 2532 removed outlier: 5.183A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2558 removed outlier: 3.597A pdb=" N ILE D2545 " --> pdb=" O HIS D2541 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.265A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2603 through 2618 Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.156A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 removed outlier: 3.779A pdb=" N LEU D2666 " --> pdb=" O PHE D2662 " (cutoff:3.500A) Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2697 removed outlier: 5.156A pdb=" N SER D2697 " --> pdb=" O SER D2693 " (cutoff:3.500A) Processing helix chain 'D' and resid 2716 through 2740 removed outlier: 4.438A pdb=" N PHE D2720 " --> pdb=" O LYS D2716 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS D2723 " --> pdb=" O TYR D2719 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D2724 " --> pdb=" O PHE D2720 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU D2726 " --> pdb=" O ASN D2722 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.206A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 5.058A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TRP D2773 " --> pdb=" O GLU D2769 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 4.445A pdb=" N GLY D2786 " --> pdb=" O MET D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 3.981A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.273A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.515A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2948 removed outlier: 3.566A pdb=" N SER D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.851A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.984A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 4.314A pdb=" N GLN D3079 " --> pdb=" O LEU D3075 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.208A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3125 through 3143 Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 3.979A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 removed outlier: 3.671A pdb=" N GLY D3164 " --> pdb=" O ALA D3160 " (cutoff:3.500A) Processing helix chain 'D' and resid 3182 through 3188 removed outlier: 3.793A pdb=" N SER D3188 " --> pdb=" O TYR D3184 " (cutoff:3.500A) Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.903A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.961A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3253 removed outlier: 5.232A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 5.091A pdb=" N GLU D3251 " --> pdb=" O SER D3247 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS D3252 " --> pdb=" O ARG D3248 " (cutoff:3.500A) Processing helix chain 'D' and resid 3269 through 3288 Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 3.914A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D3300 " --> pdb=" O MET D3296 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL D3301 " --> pdb=" O LYS D3297 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.965A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3329 removed outlier: 5.000A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 4.419A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 3.640A pdb=" N MET D3605 " --> pdb=" O ALA D3601 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.668A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.265A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 3.623A pdb=" N GLU D3642 " --> pdb=" O ASP D3638 " (cutoff:3.500A) Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.879A 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 removed outlier: 3.889A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.976A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.886A 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: 4.674A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.690A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 4.148A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.650A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.651A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.513A pdb=" N PHE D4020 " --> pdb=" O PHE D4016 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.609A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.105A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.257A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.718A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.541A 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 4184 through 4208 removed outlier: 5.267A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4271 removed outlier: 3.662A pdb=" N LEU D4255 " --> pdb=" O ASN D4251 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D4260 " --> pdb=" O MET D4256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D4261 " --> pdb=" O ARG D4257 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER D4263 " --> pdb=" O LEU D4259 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU D4264 " --> pdb=" O SER D4260 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS D4265 " --> pdb=" O LEU D4261 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS D4269 " --> pdb=" O LYS D4265 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.836A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.033A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 4.240A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.425A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.471A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 3.846A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4701 removed outlier: 3.890A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.865A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.704A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.901A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.376A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.908A 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: 4.059A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.338A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.984A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.968A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 4.786A pdb=" N ILE D3180 " --> pdb=" O LYS D3177 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 4.960A pdb=" N ILE D2382 " --> pdb=" O GLU D2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.071A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.761A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.071A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.761A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.071A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.761A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.071A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.761A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.984A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.514A 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: 6.639A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.087A 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 removed outlier: 3.715A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.972A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 307 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 7, first strand: chain 'A' and resid 370 through 374 removed outlier: 3.626A pdb=" N TRP A 371 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.776A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.842A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A1617 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.557A pdb=" N MET A 778 " --> pdb=" O THR A1468 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A1478 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.273A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 948 through 952 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 7.311A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1284 removed outlier: 6.275A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.861A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 17, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.636A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.983A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.513A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.639A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 160 through 165 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.716A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.971A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 307 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 24, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.627A pdb=" N TRP B 371 " --> pdb=" O HIS B 394 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.775A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.841A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B1617 " --> pdb=" O PHE B 802 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.557A pdb=" N MET B 778 " --> pdb=" O THR B1468 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B1478 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.272A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 948 through 952 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 7.311A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1280 through 1284 removed outlier: 6.275A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.861A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 34, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.637A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.984A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.639A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 160 through 165 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.715A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.972A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 307 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 41, first strand: chain 'C' and resid 370 through 374 removed outlier: 3.625A pdb=" N TRP C 371 " --> pdb=" O HIS C 394 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.776A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.842A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C1617 " --> pdb=" O PHE C 802 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.557A pdb=" N MET C 778 " --> pdb=" O THR C1468 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C1478 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.272A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 948 through 952 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 7.311A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 1280 through 1284 removed outlier: 6.275A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.861A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 51, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.636A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.984A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.639A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'D' and resid 160 through 165 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.715A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.971A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 307 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 58, first strand: chain 'D' and resid 370 through 374 removed outlier: 3.626A pdb=" N TRP D 371 " --> pdb=" O HIS D 394 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.776A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.841A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D1617 " --> pdb=" O PHE D 802 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.557A pdb=" N MET D 778 " --> pdb=" O THR D1468 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D1478 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.272A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 948 through 952 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 7.311A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 1280 through 1284 removed outlier: 6.275A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.861A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 68, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.637A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.574A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'E' and resid 22 through 25 removed outlier: 4.123A pdb=" N THR E 22 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.573A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'F' and resid 22 through 25 removed outlier: 4.123A pdb=" N THR F 22 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.574A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'G' and resid 22 through 25 removed outlier: 4.123A pdb=" N THR G 22 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.574A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'H' and resid 22 through 25 removed outlier: 4.123A pdb=" N THR H 22 " --> pdb=" O GLU H 108 " (cutoff:3.500A) 7324 hydrogen bonds defined for protein. 21844 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: 101.94 Time building geometry restraints manager: 44.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 43495 1.34 - 1.46: 24197 1.46 - 1.58: 72476 1.58 - 1.70: 40 1.70 - 1.82: 1520 Bond restraints: 141728 Sorted by residual: bond pdb=" C03 KVR C5004 " pdb=" O02 KVR C5004 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C03 KVR D5004 " pdb=" O02 KVR D5004 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C03 KVR B5004 " pdb=" O02 KVR B5004 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" C03 KVR A5004 " pdb=" O02 KVR A5004 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" C06 KVR D5004 " pdb=" S09 KVR D5004 " ideal model delta sigma weight residual 1.767 1.820 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 141723 not shown) Histogram of bond angle deviations from ideal: 95.35 - 104.26: 2226 104.26 - 113.17: 77273 113.17 - 122.08: 87149 122.08 - 130.99: 24118 130.99 - 139.90: 726 Bond angle restraints: 191492 Sorted by residual: angle pdb=" CB MET B2004 " pdb=" CG MET B2004 " pdb=" SD MET B2004 " ideal model delta sigma weight residual 112.70 129.27 -16.57 3.00e+00 1.11e-01 3.05e+01 angle pdb=" CB MET A2004 " pdb=" CG MET A2004 " pdb=" SD MET A2004 " ideal model delta sigma weight residual 112.70 129.24 -16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" CB MET C2004 " pdb=" CG MET C2004 " pdb=" SD MET C2004 " ideal model delta sigma weight residual 112.70 129.23 -16.53 3.00e+00 1.11e-01 3.03e+01 angle pdb=" CB MET D2004 " pdb=" CG MET D2004 " pdb=" SD MET D2004 " ideal model delta sigma weight residual 112.70 129.22 -16.52 3.00e+00 1.11e-01 3.03e+01 angle pdb=" C VAL A 894 " pdb=" N MET A 895 " pdb=" CA MET A 895 " ideal model delta sigma weight residual 122.26 113.86 8.40 1.59e+00 3.96e-01 2.79e+01 ... (remaining 191487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 82207 28.61 - 57.22: 2918 57.22 - 85.84: 351 85.84 - 114.45: 4 114.45 - 143.06: 12 Dihedral angle restraints: 85492 sinusoidal: 35132 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 -134.12 -45.88 0 5.00e+00 4.00e-02 8.42e+01 dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual -180.00 -134.12 -45.88 0 5.00e+00 4.00e-02 8.42e+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 -134.13 -45.87 0 5.00e+00 4.00e-02 8.42e+01 ... (remaining 85489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 19474 0.080 - 0.160: 1463 0.160 - 0.240: 43 0.240 - 0.320: 4 0.320 - 0.401: 4 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE C2478 " pdb=" CA ILE C2478 " pdb=" CG1 ILE C2478 " pdb=" CG2 ILE C2478 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE D2478 " pdb=" CA ILE D2478 " pdb=" CG1 ILE D2478 " pdb=" CG2 ILE D2478 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE A2478 " pdb=" CA ILE A2478 " pdb=" CG1 ILE A2478 " pdb=" CG2 ILE A2478 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 20985 not shown) Planarity restraints: 24600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " 0.106 5.00e-02 4.00e+02 1.64e-01 4.31e+01 pdb=" N PRO B4641 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " -0.106 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO A4641 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D4640 " -0.106 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO D4641 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO D4641 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO D4641 " -0.082 5.00e-02 4.00e+02 ... (remaining 24597 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1409 2.62 - 3.19: 129828 3.19 - 3.76: 229977 3.76 - 4.33: 314487 4.33 - 4.90: 506117 Nonbonded interactions: 1181818 Sorted by model distance: nonbonded pdb=" O THR A1548 " pdb=" OG1 THR D2832 " model vdw 2.054 2.440 nonbonded pdb=" OG1 THR A2832 " pdb=" O THR B1548 " model vdw 2.093 2.440 nonbonded pdb=" OG1 THR C2832 " pdb=" O THR D1548 " model vdw 2.093 2.440 nonbonded pdb=" O ILE E 51 " pdb=" NZ LYS E 53 " model vdw 2.110 2.520 nonbonded pdb=" O ILE G 51 " pdb=" NZ LYS G 53 " model vdw 2.111 2.520 ... (remaining 1181813 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 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.600 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: 0.140 Extract box with map and model: 30.490 Check model and map are aligned: 1.490 Set scattering table: 0.960 Process input model: 445.150 Find NCS groups from input model: 7.720 Set up NCS constraints: 1.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 495.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 0.057 141728 Z= 0.213 Angle : 0.737 18.426 191492 Z= 0.413 Chirality : 0.042 0.401 20988 Planarity : 0.006 0.195 24600 Dihedral : 14.116 143.061 53016 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 0.18 % Allowed : 0.40 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.06), residues: 17212 helix: 1.30 (0.06), residues: 8936 sheet: 0.18 (0.13), residues: 1620 loop : -0.48 (0.07), residues: 6656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C3250 HIS 0.022 0.001 HIS C3034 PHE 0.049 0.002 PHE D3117 TYR 0.023 0.001 TYR C4250 ARG 0.011 0.001 ARG B3043 *********************** 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 1166 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1138 time to evaluate : 11.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8227 (tmm) cc_final: 0.7832 (tmm) REVERT: A 655 MET cc_start: 0.8512 (mmm) cc_final: 0.8139 (mmm) REVERT: A 895 MET cc_start: 0.9097 (pmm) cc_final: 0.8585 (pmm) REVERT: A 940 LEU cc_start: 0.9476 (mt) cc_final: 0.9203 (mt) REVERT: A 995 MET cc_start: 0.8747 (ttp) cc_final: 0.8499 (ttm) REVERT: A 2602 HIS cc_start: 0.8778 (m-70) cc_final: 0.8357 (m-70) REVERT: A 2640 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9085 (tp) REVERT: A 2840 MET cc_start: 0.8363 (tpp) cc_final: 0.8090 (mmt) REVERT: A 2843 MET cc_start: 0.8936 (ptt) cc_final: 0.8539 (ppp) REVERT: A 2844 MET cc_start: 0.8770 (ppp) cc_final: 0.8493 (ppp) REVERT: A 2887 GLU cc_start: 0.8892 (pp20) cc_final: 0.8664 (pp20) REVERT: A 2890 GLN cc_start: 0.8938 (mp10) cc_final: 0.8623 (mp10) REVERT: A 2893 LEU cc_start: 0.9557 (mp) cc_final: 0.9308 (mp) REVERT: A 2895 PHE cc_start: 0.8655 (t80) cc_final: 0.8104 (t80) REVERT: A 2897 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 2921 PHE cc_start: 0.8681 (t80) cc_final: 0.8369 (t80) REVERT: A 2926 LEU cc_start: 0.9614 (mt) cc_final: 0.9375 (mt) REVERT: A 2932 TYR cc_start: 0.8196 (t80) cc_final: 0.7807 (t80) REVERT: A 2943 PHE cc_start: 0.7802 (m-80) cc_final: 0.7531 (m-80) REVERT: A 2982 PHE cc_start: 0.8681 (m-80) cc_final: 0.8155 (m-80) REVERT: A 3003 MET cc_start: 0.8617 (ptm) cc_final: 0.8045 (ptm) REVERT: A 3022 PHE cc_start: 0.7889 (m-80) cc_final: 0.7622 (m-10) REVERT: A 3031 ASN cc_start: 0.9203 (t0) cc_final: 0.8801 (t0) REVERT: A 3131 TYR cc_start: 0.8701 (m-80) cc_final: 0.8041 (m-80) REVERT: A 3138 TYR cc_start: 0.9279 (t80) cc_final: 0.8853 (t80) REVERT: A 3162 PHE cc_start: 0.8839 (t80) cc_final: 0.8571 (t80) REVERT: A 3241 MET cc_start: 0.9007 (mmp) cc_final: 0.8359 (mmt) REVERT: A 3246 MET cc_start: 0.9116 (mtp) cc_final: 0.8785 (mtm) REVERT: A 3302 PHE cc_start: 0.9020 (m-80) cc_final: 0.8726 (m-80) REVERT: A 3304 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8822 (tp-100) REVERT: A 3819 MET cc_start: 0.6906 (mtm) cc_final: 0.6535 (mtm) REVERT: A 4046 ARG cc_start: 0.8446 (tpm170) cc_final: 0.7887 (tpm170) REVERT: A 4258 MET cc_start: 0.8680 (mtp) cc_final: 0.8134 (ptt) REVERT: A 4707 MET cc_start: 0.8559 (ttp) cc_final: 0.8213 (ttp) REVERT: E 4 GLU cc_start: 0.7989 (mp0) cc_final: 0.7753 (mp0) REVERT: E 18 LYS cc_start: 0.9085 (mppt) cc_final: 0.8848 (mppt) REVERT: F 18 LYS cc_start: 0.9145 (mppt) cc_final: 0.8811 (mppt) REVERT: F 62 GLU cc_start: 0.7913 (pm20) cc_final: 0.7691 (pm20) REVERT: G 4 GLU cc_start: 0.7876 (mp0) cc_final: 0.7637 (mp0) REVERT: G 58 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8066 (ttpp) REVERT: G 62 GLU cc_start: 0.7969 (pm20) cc_final: 0.7606 (pm20) REVERT: H 18 LYS cc_start: 0.9082 (mppt) cc_final: 0.8757 (mppt) REVERT: B 81 MET cc_start: 0.8191 (tmm) cc_final: 0.7750 (tmm) REVERT: B 655 MET cc_start: 0.8570 (mmm) cc_final: 0.8221 (mmm) REVERT: B 895 MET cc_start: 0.9128 (pmm) cc_final: 0.8594 (pmm) REVERT: B 940 LEU cc_start: 0.9493 (mt) cc_final: 0.9220 (mt) REVERT: B 995 MET cc_start: 0.8772 (ttp) cc_final: 0.8519 (ttm) REVERT: B 1060 TYR cc_start: 0.8173 (t80) cc_final: 0.7880 (t80) REVERT: B 2602 HIS cc_start: 0.8800 (m-70) cc_final: 0.8369 (m-70) REVERT: B 2640 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9077 (tp) REVERT: B 2779 LEU cc_start: 0.9440 (mp) cc_final: 0.9167 (mp) REVERT: B 2783 LEU cc_start: 0.9411 (tt) cc_final: 0.9182 (mm) REVERT: B 2837 LEU cc_start: 0.9531 (mt) cc_final: 0.9326 (mt) REVERT: B 2840 MET cc_start: 0.8295 (tpp) cc_final: 0.7374 (mmt) REVERT: B 2843 MET cc_start: 0.8937 (ptt) cc_final: 0.8509 (ppp) REVERT: B 2844 MET cc_start: 0.8779 (ppp) cc_final: 0.8293 (ppp) REVERT: B 2887 GLU cc_start: 0.8912 (pp20) cc_final: 0.8664 (pp20) REVERT: B 2893 LEU cc_start: 0.9561 (mp) cc_final: 0.9305 (mp) REVERT: B 2895 PHE cc_start: 0.8603 (t80) cc_final: 0.8005 (t80) REVERT: B 2897 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 2921 PHE cc_start: 0.8672 (t80) cc_final: 0.8342 (t80) REVERT: B 2926 LEU cc_start: 0.9606 (mt) cc_final: 0.9377 (mt) REVERT: B 2932 TYR cc_start: 0.8163 (t80) cc_final: 0.7811 (t80) REVERT: B 2982 PHE cc_start: 0.8680 (m-80) cc_final: 0.8164 (m-80) REVERT: B 3003 MET cc_start: 0.8619 (ptm) cc_final: 0.8068 (ptm) REVERT: B 3022 PHE cc_start: 0.7859 (m-80) cc_final: 0.7590 (m-10) REVERT: B 3031 ASN cc_start: 0.9213 (t0) cc_final: 0.8786 (t0) REVERT: B 3104 MET cc_start: 0.8276 (ptt) cc_final: 0.8051 (ptt) REVERT: B 3109 PHE cc_start: 0.9188 (m-10) cc_final: 0.8865 (m-10) REVERT: B 3131 TYR cc_start: 0.8731 (m-80) cc_final: 0.8463 (m-10) REVERT: B 3138 TYR cc_start: 0.9288 (t80) cc_final: 0.8845 (t80) REVERT: B 3162 PHE cc_start: 0.8842 (t80) cc_final: 0.8454 (t80) REVERT: B 3241 MET cc_start: 0.8969 (mmp) cc_final: 0.8285 (mmt) REVERT: B 3246 MET cc_start: 0.9111 (mtp) cc_final: 0.8772 (mtm) REVERT: B 3250 TRP cc_start: 0.8933 (t-100) cc_final: 0.8688 (t-100) REVERT: B 3302 PHE cc_start: 0.9016 (m-80) cc_final: 0.8692 (m-80) REVERT: B 3304 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8812 (tp-100) REVERT: B 3819 MET cc_start: 0.6785 (mtm) cc_final: 0.6502 (mtm) REVERT: B 4046 ARG cc_start: 0.8476 (tpm170) cc_final: 0.7913 (tpm170) REVERT: B 4258 MET cc_start: 0.8685 (mtp) cc_final: 0.8155 (ptt) REVERT: B 4707 MET cc_start: 0.8569 (ttp) cc_final: 0.8299 (ttt) REVERT: C 81 MET cc_start: 0.8197 (tmm) cc_final: 0.7753 (tmm) REVERT: C 655 MET cc_start: 0.8604 (mmm) cc_final: 0.8225 (mmm) REVERT: C 895 MET cc_start: 0.9125 (pmm) cc_final: 0.8601 (pmm) REVERT: C 940 LEU cc_start: 0.9493 (mt) cc_final: 0.9225 (mt) REVERT: C 995 MET cc_start: 0.8774 (ttp) cc_final: 0.8512 (ttm) REVERT: C 1975 MET cc_start: 0.8595 (ptt) cc_final: 0.8382 (ptt) REVERT: C 2602 HIS cc_start: 0.8820 (m-70) cc_final: 0.8526 (m-70) REVERT: C 2640 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9085 (tp) REVERT: C 2779 LEU cc_start: 0.9467 (mp) cc_final: 0.9180 (mp) REVERT: C 2840 MET cc_start: 0.8335 (tpp) cc_final: 0.7758 (mmt) REVERT: C 2843 MET cc_start: 0.8896 (ptt) cc_final: 0.8518 (ppp) REVERT: C 2844 MET cc_start: 0.8775 (ppp) cc_final: 0.8303 (ppp) REVERT: C 2887 GLU cc_start: 0.8931 (pp20) cc_final: 0.8696 (pp20) REVERT: C 2893 LEU cc_start: 0.9565 (mp) cc_final: 0.9305 (mp) REVERT: C 2895 PHE cc_start: 0.8607 (t80) cc_final: 0.8053 (t80) REVERT: C 2897 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8784 (tm-30) REVERT: C 2921 PHE cc_start: 0.8651 (t80) cc_final: 0.8334 (t80) REVERT: C 2932 TYR cc_start: 0.8159 (t80) cc_final: 0.7808 (t80) REVERT: C 2943 PHE cc_start: 0.7857 (m-80) cc_final: 0.7651 (m-80) REVERT: C 2982 PHE cc_start: 0.8687 (m-80) cc_final: 0.8200 (m-80) REVERT: C 3003 MET cc_start: 0.8653 (ptm) cc_final: 0.8117 (ptm) REVERT: C 3022 PHE cc_start: 0.7872 (m-80) cc_final: 0.7582 (m-10) REVERT: C 3031 ASN cc_start: 0.9202 (t0) cc_final: 0.8865 (t0) REVERT: C 3104 MET cc_start: 0.8260 (ptt) cc_final: 0.8032 (ptt) REVERT: C 3109 PHE cc_start: 0.9214 (m-10) cc_final: 0.8872 (m-10) REVERT: C 3131 TYR cc_start: 0.8759 (m-80) cc_final: 0.8517 (m-80) REVERT: C 3138 TYR cc_start: 0.9289 (t80) cc_final: 0.8852 (t80) REVERT: C 3162 PHE cc_start: 0.8765 (t80) cc_final: 0.8423 (t80) REVERT: C 3241 MET cc_start: 0.8990 (mmp) cc_final: 0.8347 (mmm) REVERT: C 3246 MET cc_start: 0.9090 (mtp) cc_final: 0.8771 (mtm) REVERT: C 3250 TRP cc_start: 0.8922 (t-100) cc_final: 0.8637 (t-100) REVERT: C 3302 PHE cc_start: 0.9013 (m-80) cc_final: 0.8677 (m-80) REVERT: C 3304 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8823 (tp-100) REVERT: C 3819 MET cc_start: 0.6851 (mtm) cc_final: 0.6645 (mtm) REVERT: C 4046 ARG cc_start: 0.8458 (tpm170) cc_final: 0.7882 (tpm170) REVERT: C 4258 MET cc_start: 0.8688 (mtp) cc_final: 0.8174 (ptt) REVERT: C 4698 LEU cc_start: 0.8595 (mt) cc_final: 0.8395 (mt) REVERT: C 4707 MET cc_start: 0.8556 (ttp) cc_final: 0.8196 (ttp) REVERT: D 81 MET cc_start: 0.8201 (tmm) cc_final: 0.7757 (tmm) REVERT: D 655 MET cc_start: 0.8575 (mmm) cc_final: 0.8232 (mmm) REVERT: D 895 MET cc_start: 0.9149 (pmm) cc_final: 0.8626 (pmm) REVERT: D 940 LEU cc_start: 0.9498 (mt) cc_final: 0.9220 (mt) REVERT: D 995 MET cc_start: 0.8805 (ttp) cc_final: 0.8546 (ttm) REVERT: D 1975 MET cc_start: 0.8599 (ptt) cc_final: 0.8385 (ptt) REVERT: D 2602 HIS cc_start: 0.8804 (m-70) cc_final: 0.8377 (m-70) REVERT: D 2640 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9049 (tp) REVERT: D 2779 LEU cc_start: 0.9450 (mp) cc_final: 0.9208 (mp) REVERT: D 2783 LEU cc_start: 0.9408 (tt) cc_final: 0.9189 (mm) REVERT: D 2840 MET cc_start: 0.8285 (tpp) cc_final: 0.7684 (mmt) REVERT: D 2843 MET cc_start: 0.8919 (ptt) cc_final: 0.8515 (ppp) REVERT: D 2844 MET cc_start: 0.8775 (ppp) cc_final: 0.8319 (ppp) REVERT: D 2887 GLU cc_start: 0.8908 (pp20) cc_final: 0.8657 (pp20) REVERT: D 2893 LEU cc_start: 0.9556 (mp) cc_final: 0.9305 (mp) REVERT: D 2895 PHE cc_start: 0.8586 (t80) cc_final: 0.8105 (t80) REVERT: D 2897 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8779 (tm-30) REVERT: D 2921 PHE cc_start: 0.8702 (t80) cc_final: 0.8362 (t80) REVERT: D 2932 TYR cc_start: 0.8148 (t80) cc_final: 0.7802 (t80) REVERT: D 2943 PHE cc_start: 0.7784 (m-80) cc_final: 0.7578 (m-80) REVERT: D 2982 PHE cc_start: 0.8685 (m-80) cc_final: 0.8159 (m-80) REVERT: D 3003 MET cc_start: 0.8618 (ptm) cc_final: 0.8060 (ptm) REVERT: D 3022 PHE cc_start: 0.7842 (m-80) cc_final: 0.7587 (m-10) REVERT: D 3031 ASN cc_start: 0.9204 (t0) cc_final: 0.8819 (t0) REVERT: D 3104 MET cc_start: 0.8233 (ptt) cc_final: 0.8011 (ptt) REVERT: D 3109 PHE cc_start: 0.9197 (m-10) cc_final: 0.8852 (m-10) REVERT: D 3138 TYR cc_start: 0.9306 (t80) cc_final: 0.8878 (t80) REVERT: D 3162 PHE cc_start: 0.8860 (t80) cc_final: 0.8472 (t80) REVERT: D 3241 MET cc_start: 0.8988 (mmp) cc_final: 0.8310 (mmm) REVERT: D 3246 MET cc_start: 0.9127 (mtp) cc_final: 0.8806 (mtm) REVERT: D 3250 TRP cc_start: 0.8918 (t-100) cc_final: 0.8654 (t-100) REVERT: D 3302 PHE cc_start: 0.9015 (m-80) cc_final: 0.8691 (m-80) REVERT: D 3304 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8812 (tp-100) REVERT: D 3819 MET cc_start: 0.6835 (mtm) cc_final: 0.6612 (mtm) REVERT: D 4046 ARG cc_start: 0.8479 (tpm170) cc_final: 0.7908 (tpm170) REVERT: D 4258 MET cc_start: 0.8667 (mtp) cc_final: 0.8148 (ptt) REVERT: D 4698 LEU cc_start: 0.8612 (mt) cc_final: 0.8408 (mt) REVERT: D 4707 MET cc_start: 0.8562 (ttp) cc_final: 0.8198 (ttp) outliers start: 28 outliers final: 8 residues processed: 1139 average time/residue: 1.2208 time to fit residues: 2425.3614 Evaluate side-chains 1030 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1018 time to evaluate : 11.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2640 LEU Chi-restraints excluded: chain A residue 4809 MET Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain B residue 2640 LEU Chi-restraints excluded: chain B residue 4809 MET Chi-restraints excluded: chain C residue 2640 LEU Chi-restraints excluded: chain C residue 4809 MET Chi-restraints excluded: chain D residue 2640 LEU Chi-restraints excluded: chain D residue 4809 MET 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: 8.9990 chunk 726 optimal weight: 9.9990 chunk 447 optimal weight: 7.9990 chunk 883 optimal weight: 4.9990 chunk 699 optimal weight: 7.9990 chunk 1354 optimal weight: 8.9990 chunk 524 optimal weight: 10.0000 chunk 823 optimal weight: 0.5980 chunk 1008 optimal weight: 8.9990 chunk 1569 optimal weight: 3.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A1626 GLN A2309 ASN A2692 GLN ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4489 GLN ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN B 635 ASN B1267 HIS B1626 GLN B2309 ASN B2692 GLN ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4489 GLN ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1267 HIS C1626 GLN C2309 ASN C2692 GLN ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4489 GLN ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN D2309 ASN D2692 GLN ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 141728 Z= 0.376 Angle : 0.682 17.374 191492 Z= 0.341 Chirality : 0.044 0.300 20988 Planarity : 0.005 0.152 24600 Dihedral : 7.101 116.550 19144 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 0.34 % Allowed : 4.10 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.06), residues: 17212 helix: 1.51 (0.06), residues: 8892 sheet: 0.02 (0.13), residues: 1680 loop : -0.42 (0.07), residues: 6640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D3250 HIS 0.021 0.001 HIS B3034 PHE 0.032 0.002 PHE A3109 TYR 0.023 0.002 TYR D2719 ARG 0.014 0.001 ARG B3260 *********************** 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 1135 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1084 time to evaluate : 11.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8294 (tmm) cc_final: 0.7880 (tmm) REVERT: A 317 MET cc_start: 0.6727 (mmm) cc_final: 0.6525 (mmm) REVERT: A 655 MET cc_start: 0.8681 (mmm) cc_final: 0.8227 (mmm) REVERT: A 895 MET cc_start: 0.9144 (pmm) cc_final: 0.8852 (pmm) REVERT: A 995 MET cc_start: 0.8807 (ttp) cc_final: 0.8547 (ttm) REVERT: A 2602 HIS cc_start: 0.8858 (m-70) cc_final: 0.8565 (m-70) REVERT: A 2610 LEU cc_start: 0.9417 (mm) cc_final: 0.9190 (mm) REVERT: A 2734 MET cc_start: 0.8986 (mmp) cc_final: 0.8565 (mmp) REVERT: A 2779 LEU cc_start: 0.9475 (mp) cc_final: 0.9027 (pt) REVERT: A 2840 MET cc_start: 0.8433 (tpp) cc_final: 0.7835 (mmt) REVERT: A 2843 MET cc_start: 0.9034 (ptt) cc_final: 0.8625 (ppp) REVERT: A 2844 MET cc_start: 0.8861 (ppp) cc_final: 0.8368 (ppp) REVERT: A 2887 GLU cc_start: 0.8881 (pp20) cc_final: 0.8652 (pp20) REVERT: A 2895 PHE cc_start: 0.8662 (t80) cc_final: 0.8286 (t80) REVERT: A 2897 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 2921 PHE cc_start: 0.8745 (t80) cc_final: 0.8270 (t80) REVERT: A 2926 LEU cc_start: 0.9641 (mt) cc_final: 0.9264 (tp) REVERT: A 2932 TYR cc_start: 0.8256 (t80) cc_final: 0.7889 (t80) REVERT: A 2963 PHE cc_start: 0.9169 (t80) cc_final: 0.8888 (t80) REVERT: A 2982 PHE cc_start: 0.8835 (m-80) cc_final: 0.8147 (m-80) REVERT: A 3003 MET cc_start: 0.8668 (ptm) cc_final: 0.8311 (ptm) REVERT: A 3022 PHE cc_start: 0.8033 (m-80) cc_final: 0.7748 (m-80) REVERT: A 3031 ASN cc_start: 0.9239 (t0) cc_final: 0.8777 (t0) REVERT: A 3069 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: A 3138 TYR cc_start: 0.9298 (t80) cc_final: 0.8871 (t80) REVERT: A 3159 LEU cc_start: 0.8922 (pp) cc_final: 0.8035 (pp) REVERT: A 3162 PHE cc_start: 0.8928 (t80) cc_final: 0.8585 (t80) REVERT: A 3241 MET cc_start: 0.9123 (mmp) cc_final: 0.8460 (mmm) REVERT: A 3246 MET cc_start: 0.9108 (mtp) cc_final: 0.8862 (mtm) REVERT: A 3302 PHE cc_start: 0.9033 (m-80) cc_final: 0.8722 (m-80) REVERT: A 3304 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8678 (tp-100) REVERT: A 4046 ARG cc_start: 0.8514 (tpm170) cc_final: 0.8053 (tpm170) REVERT: A 4258 MET cc_start: 0.8686 (mtp) cc_final: 0.8144 (ptt) REVERT: A 4481 TRP cc_start: 0.7279 (m-90) cc_final: 0.6795 (m-90) REVERT: A 4707 MET cc_start: 0.8615 (ttp) cc_final: 0.8370 (ttt) REVERT: A 4726 MET cc_start: 0.8444 (tpt) cc_final: 0.7838 (tpp) REVERT: A 4809 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8841 (mmm) REVERT: E 4 GLU cc_start: 0.7750 (mp0) cc_final: 0.7417 (mp0) REVERT: E 18 LYS cc_start: 0.9148 (mppt) cc_final: 0.8930 (mppt) REVERT: F 18 LYS cc_start: 0.9221 (mppt) cc_final: 0.8936 (mppt) REVERT: F 58 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7976 (ttpp) REVERT: G 4 GLU cc_start: 0.7687 (mp0) cc_final: 0.7430 (mp0) REVERT: G 14 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8554 (ptp90) REVERT: G 58 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8147 (ttpp) REVERT: H 18 LYS cc_start: 0.9170 (mppt) cc_final: 0.8893 (mppt) REVERT: B 81 MET cc_start: 0.8245 (tmm) cc_final: 0.7781 (tmm) REVERT: B 895 MET cc_start: 0.9183 (pmm) cc_final: 0.8896 (pmm) REVERT: B 995 MET cc_start: 0.8832 (ttp) cc_final: 0.8574 (ttm) REVERT: B 1060 TYR cc_start: 0.8271 (t80) cc_final: 0.7994 (t80) REVERT: B 2585 MET cc_start: 0.7875 (ppp) cc_final: 0.7673 (ppp) REVERT: B 2602 HIS cc_start: 0.8887 (m-70) cc_final: 0.8573 (m-70) REVERT: B 2689 MET cc_start: 0.6607 (mtt) cc_final: 0.6214 (mtp) REVERT: B 2734 MET cc_start: 0.8995 (mmp) cc_final: 0.8580 (mmp) REVERT: B 2779 LEU cc_start: 0.9441 (mp) cc_final: 0.9122 (mp) REVERT: B 2837 LEU cc_start: 0.9555 (mt) cc_final: 0.9345 (mt) REVERT: B 2840 MET cc_start: 0.8910 (tpp) cc_final: 0.8388 (tpp) REVERT: B 2843 MET cc_start: 0.8972 (ptt) cc_final: 0.8610 (ppp) REVERT: B 2844 MET cc_start: 0.8873 (ppp) cc_final: 0.8504 (ppp) REVERT: B 2890 GLN cc_start: 0.8924 (mp10) cc_final: 0.8556 (mp10) REVERT: B 2893 LEU cc_start: 0.9583 (mp) cc_final: 0.9378 (mt) REVERT: B 2895 PHE cc_start: 0.8643 (t80) cc_final: 0.8230 (t80) REVERT: B 2897 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8784 (tm-30) REVERT: B 2921 PHE cc_start: 0.8757 (t80) cc_final: 0.8283 (t80) REVERT: B 2926 LEU cc_start: 0.9634 (mt) cc_final: 0.9396 (mt) REVERT: B 2932 TYR cc_start: 0.8235 (t80) cc_final: 0.7919 (t80) REVERT: B 2982 PHE cc_start: 0.8796 (m-80) cc_final: 0.8191 (m-80) REVERT: B 3003 MET cc_start: 0.8721 (ptm) cc_final: 0.8260 (ptm) REVERT: B 3022 PHE cc_start: 0.7993 (m-80) cc_final: 0.7725 (m-80) REVERT: B 3031 ASN cc_start: 0.9185 (t0) cc_final: 0.8845 (t0) REVERT: B 3069 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: B 3109 PHE cc_start: 0.9269 (m-10) cc_final: 0.8798 (m-80) REVERT: B 3138 TYR cc_start: 0.9302 (t80) cc_final: 0.8886 (t80) REVERT: B 3152 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.7997 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8911 (pp) cc_final: 0.8028 (pp) REVERT: B 3162 PHE cc_start: 0.8933 (t80) cc_final: 0.8356 (t80) REVERT: B 3171 LEU cc_start: 0.9046 (tp) cc_final: 0.8842 (tp) REVERT: B 3241 MET cc_start: 0.9106 (mmp) cc_final: 0.8390 (mmm) REVERT: B 3246 MET cc_start: 0.9108 (mtp) cc_final: 0.8847 (mtm) REVERT: B 3250 TRP cc_start: 0.8891 (t-100) cc_final: 0.8688 (t-100) REVERT: B 3302 PHE cc_start: 0.9021 (m-80) cc_final: 0.8723 (m-80) REVERT: B 3304 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8785 (tp-100) REVERT: B 4046 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8095 (tpm170) REVERT: B 4258 MET cc_start: 0.8688 (mtp) cc_final: 0.8171 (ptt) REVERT: B 4698 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 4707 MET cc_start: 0.8637 (ttp) cc_final: 0.8395 (ttt) REVERT: B 4726 MET cc_start: 0.8430 (tpt) cc_final: 0.7817 (tpp) REVERT: C 81 MET cc_start: 0.8263 (tmm) cc_final: 0.7815 (tmm) REVERT: C 895 MET cc_start: 0.9156 (pmm) cc_final: 0.8857 (pmm) REVERT: C 940 LEU cc_start: 0.9492 (mt) cc_final: 0.9257 (pp) REVERT: C 995 MET cc_start: 0.8815 (ttp) cc_final: 0.8559 (ttm) REVERT: C 1051 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8259 (mtt180) REVERT: C 2485 LEU cc_start: 0.9440 (mm) cc_final: 0.9226 (mm) REVERT: C 2585 MET cc_start: 0.7884 (ppp) cc_final: 0.7682 (ppp) REVERT: C 2602 HIS cc_start: 0.8883 (m-70) cc_final: 0.8580 (m-70) REVERT: C 2734 MET cc_start: 0.8992 (mmp) cc_final: 0.8596 (mmp) REVERT: C 2779 LEU cc_start: 0.9410 (mp) cc_final: 0.9202 (mp) REVERT: C 2840 MET cc_start: 0.8439 (tpp) cc_final: 0.7516 (mmt) REVERT: C 2843 MET cc_start: 0.8957 (ptt) cc_final: 0.8533 (ppp) REVERT: C 2844 MET cc_start: 0.8866 (ppp) cc_final: 0.8369 (ppp) REVERT: C 2890 GLN cc_start: 0.8931 (mp10) cc_final: 0.8593 (mp10) REVERT: C 2895 PHE cc_start: 0.8699 (t80) cc_final: 0.8160 (t80) REVERT: C 2897 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8776 (tm-30) REVERT: C 2921 PHE cc_start: 0.8752 (t80) cc_final: 0.8275 (t80) REVERT: C 2932 TYR cc_start: 0.8224 (t80) cc_final: 0.7909 (t80) REVERT: C 2982 PHE cc_start: 0.8830 (m-80) cc_final: 0.8273 (m-80) REVERT: C 3003 MET cc_start: 0.8729 (ptm) cc_final: 0.8267 (ptm) REVERT: C 3022 PHE cc_start: 0.8027 (m-80) cc_final: 0.7728 (m-80) REVERT: C 3031 ASN cc_start: 0.9234 (t0) cc_final: 0.8794 (t0) REVERT: C 3069 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8377 (mm-30) REVERT: C 3109 PHE cc_start: 0.9255 (m-10) cc_final: 0.8761 (m-80) REVERT: C 3138 TYR cc_start: 0.9302 (t80) cc_final: 0.8895 (t80) REVERT: C 3152 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.8075 (ptp-170) REVERT: C 3162 PHE cc_start: 0.8879 (t80) cc_final: 0.8327 (t80) REVERT: C 3241 MET cc_start: 0.9085 (mmp) cc_final: 0.8415 (mmt) REVERT: C 3246 MET cc_start: 0.9109 (mtp) cc_final: 0.8838 (mtm) REVERT: C 3250 TRP cc_start: 0.8895 (t-100) cc_final: 0.8691 (t-100) REVERT: C 3302 PHE cc_start: 0.9013 (m-80) cc_final: 0.8717 (m-80) REVERT: C 3304 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8776 (tp-100) REVERT: C 4046 ARG cc_start: 0.8552 (tpm170) cc_final: 0.8058 (tpm170) REVERT: C 4258 MET cc_start: 0.8681 (mtp) cc_final: 0.8155 (ptt) REVERT: C 4698 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8359 (mt) REVERT: C 4707 MET cc_start: 0.8626 (ttp) cc_final: 0.8386 (ttt) REVERT: C 4726 MET cc_start: 0.8459 (tpt) cc_final: 0.7841 (tpp) REVERT: D 81 MET cc_start: 0.8259 (tmm) cc_final: 0.7814 (tmm) REVERT: D 895 MET cc_start: 0.9186 (pmm) cc_final: 0.8883 (pmm) REVERT: D 940 LEU cc_start: 0.9495 (mt) cc_final: 0.9255 (pp) REVERT: D 995 MET cc_start: 0.8821 (ttp) cc_final: 0.8559 (ttm) REVERT: D 1051 ARG cc_start: 0.8565 (mtm180) cc_final: 0.8253 (mtt180) REVERT: D 2602 HIS cc_start: 0.8872 (m-70) cc_final: 0.8567 (m-70) REVERT: D 2734 MET cc_start: 0.8969 (mmp) cc_final: 0.8556 (mmp) REVERT: D 2779 LEU cc_start: 0.9468 (mp) cc_final: 0.9178 (mp) REVERT: D 2840 MET cc_start: 0.8397 (tpp) cc_final: 0.7573 (mmt) REVERT: D 2843 MET cc_start: 0.8971 (ptt) cc_final: 0.8569 (ppp) REVERT: D 2844 MET cc_start: 0.8857 (ppp) cc_final: 0.8371 (ppp) REVERT: D 2890 GLN cc_start: 0.8916 (mp10) cc_final: 0.8541 (mp10) REVERT: D 2895 PHE cc_start: 0.8757 (t80) cc_final: 0.8387 (t80) REVERT: D 2897 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8810 (tm-30) REVERT: D 2921 PHE cc_start: 0.8754 (t80) cc_final: 0.8275 (t80) REVERT: D 2932 TYR cc_start: 0.8229 (t80) cc_final: 0.7922 (t80) REVERT: D 2982 PHE cc_start: 0.8795 (m-80) cc_final: 0.8193 (m-80) REVERT: D 3003 MET cc_start: 0.8698 (ptm) cc_final: 0.8234 (ptm) REVERT: D 3022 PHE cc_start: 0.7991 (m-80) cc_final: 0.7725 (m-80) REVERT: D 3031 ASN cc_start: 0.9234 (t0) cc_final: 0.8780 (t0) REVERT: D 3069 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8391 (mm-30) REVERT: D 3109 PHE cc_start: 0.9266 (m-10) cc_final: 0.8787 (m-80) REVERT: D 3138 TYR cc_start: 0.9317 (t80) cc_final: 0.8932 (t80) REVERT: D 3162 PHE cc_start: 0.8947 (t80) cc_final: 0.8370 (t80) REVERT: D 3241 MET cc_start: 0.9093 (mmp) cc_final: 0.8437 (mmt) REVERT: D 3246 MET cc_start: 0.9123 (mtp) cc_final: 0.8882 (mtm) REVERT: D 3250 TRP cc_start: 0.8880 (t-100) cc_final: 0.8679 (t-100) REVERT: D 3302 PHE cc_start: 0.9052 (m-80) cc_final: 0.8748 (m-80) REVERT: D 3304 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8778 (tp-100) REVERT: D 4046 ARG cc_start: 0.8554 (tpm170) cc_final: 0.8045 (tpm170) REVERT: D 4258 MET cc_start: 0.8707 (mtp) cc_final: 0.8173 (ptt) REVERT: D 4698 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8373 (mt) REVERT: D 4707 MET cc_start: 0.8650 (ttp) cc_final: 0.8413 (ttt) REVERT: D 4726 MET cc_start: 0.8458 (tpt) cc_final: 0.7817 (tpp) REVERT: D 4748 MET cc_start: 0.7392 (mpp) cc_final: 0.7145 (mpp) outliers start: 51 outliers final: 26 residues processed: 1096 average time/residue: 1.1944 time to fit residues: 2298.4023 Evaluate side-chains 1062 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1028 time to evaluate : 11.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 4809 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 2880 LYS Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3053 VAL Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 4698 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 2172 MET Chi-restraints excluded: chain C residue 2880 LYS Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3053 VAL Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 2880 LYS Chi-restraints excluded: chain D residue 2980 LEU Chi-restraints excluded: chain D residue 3053 VAL Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.8980 chunk 487 optimal weight: 6.9990 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 9.9990 chunk 432 optimal weight: 0.0040 chunk 1572 optimal weight: 8.9990 chunk 1698 optimal weight: 3.9990 chunk 1400 optimal weight: 3.9990 chunk 1558 optimal weight: 3.9990 chunk 535 optimal weight: 5.9990 chunk 1261 optimal weight: 6.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN A1004 HIS A1267 HIS ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN A2224 ASN A2579 GLN A2659 GLN ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B1004 HIS ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 GLN B2224 ASN B2659 GLN B2704 GLN ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1004 HIS ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 GLN C2224 ASN C2659 GLN C2704 GLN ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3905 ASN ** C4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN D1004 HIS D1267 HIS ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN D2224 ASN D2659 GLN D2704 GLN ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 141728 Z= 0.225 Angle : 0.630 17.566 191492 Z= 0.313 Chirality : 0.041 0.221 20988 Planarity : 0.004 0.141 24600 Dihedral : 6.459 105.122 19111 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 0.45 % Allowed : 5.95 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.06), residues: 17212 helix: 1.60 (0.06), residues: 8916 sheet: 0.07 (0.13), residues: 1652 loop : -0.43 (0.07), residues: 6644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 893 HIS 0.021 0.001 HIS B3034 PHE 0.024 0.001 PHE A3109 TYR 0.039 0.001 TYR A2220 ARG 0.010 0.000 ARG B3150 *********************** 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 1128 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1060 time to evaluate : 12.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8298 (tmm) cc_final: 0.7859 (tmm) REVERT: A 655 MET cc_start: 0.8677 (mmm) cc_final: 0.8155 (mmm) REVERT: A 895 MET cc_start: 0.9214 (pmm) cc_final: 0.8894 (pmm) REVERT: A 995 MET cc_start: 0.8795 (ttp) cc_final: 0.8532 (ttm) REVERT: A 2602 HIS cc_start: 0.8854 (m-70) cc_final: 0.8539 (m-70) REVERT: A 2610 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9087 (mm) REVERT: A 2734 MET cc_start: 0.9081 (mmp) cc_final: 0.8791 (mmp) REVERT: A 2782 MET cc_start: 0.8651 (tpt) cc_final: 0.8366 (tpp) REVERT: A 2840 MET cc_start: 0.8591 (tpp) cc_final: 0.8171 (mmt) REVERT: A 2843 MET cc_start: 0.8971 (ptt) cc_final: 0.8546 (ppp) REVERT: A 2844 MET cc_start: 0.8852 (ppp) cc_final: 0.8425 (ppp) REVERT: A 2887 GLU cc_start: 0.8846 (pp20) cc_final: 0.8591 (pp20) REVERT: A 2893 LEU cc_start: 0.9608 (mt) cc_final: 0.9308 (mt) REVERT: A 2895 PHE cc_start: 0.8805 (t80) cc_final: 0.8412 (t80) REVERT: A 2897 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 2921 PHE cc_start: 0.8709 (t80) cc_final: 0.8145 (t80) REVERT: A 2926 LEU cc_start: 0.9638 (mt) cc_final: 0.9248 (tp) REVERT: A 2932 TYR cc_start: 0.8251 (t80) cc_final: 0.7935 (t80) REVERT: A 2938 GLN cc_start: 0.8899 (pp30) cc_final: 0.8507 (pp30) REVERT: A 2982 PHE cc_start: 0.8778 (m-80) cc_final: 0.8096 (m-80) REVERT: A 3003 MET cc_start: 0.8642 (ptm) cc_final: 0.8326 (ptm) REVERT: A 3022 PHE cc_start: 0.7932 (m-80) cc_final: 0.7648 (m-80) REVERT: A 3031 ASN cc_start: 0.9182 (t0) cc_final: 0.8790 (t0) REVERT: A 3069 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: A 3105 LEU cc_start: 0.8918 (mm) cc_final: 0.8613 (tp) REVERT: A 3138 TYR cc_start: 0.9291 (t80) cc_final: 0.8875 (t80) REVERT: A 3152 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8319 (ptp-170) REVERT: A 3159 LEU cc_start: 0.8902 (pp) cc_final: 0.7975 (pp) REVERT: A 3162 PHE cc_start: 0.8920 (t80) cc_final: 0.8708 (t80) REVERT: A 3241 MET cc_start: 0.9142 (mmp) cc_final: 0.8403 (mmm) REVERT: A 3246 MET cc_start: 0.9069 (mtp) cc_final: 0.8806 (mtm) REVERT: A 3302 PHE cc_start: 0.8975 (m-80) cc_final: 0.8685 (m-80) REVERT: A 3304 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8585 (tp-100) REVERT: A 4035 TYR cc_start: 0.8212 (m-80) cc_final: 0.7816 (t80) REVERT: A 4046 ARG cc_start: 0.8507 (tpm170) cc_final: 0.8111 (tpp-160) REVERT: A 4274 MET cc_start: 0.4430 (ttp) cc_final: 0.4084 (mtp) REVERT: A 4707 MET cc_start: 0.8584 (ttp) cc_final: 0.8336 (ttt) REVERT: A 4726 MET cc_start: 0.8409 (tpt) cc_final: 0.7780 (tpp) REVERT: A 4804 MET cc_start: 0.8956 (mmp) cc_final: 0.8684 (mmm) REVERT: E 4 GLU cc_start: 0.7750 (mp0) cc_final: 0.7476 (mp0) REVERT: E 18 LYS cc_start: 0.9157 (mppt) cc_final: 0.8945 (mppt) REVERT: G 14 ARG cc_start: 0.8762 (mtm110) cc_final: 0.8512 (ptp90) REVERT: G 18 LYS cc_start: 0.9065 (mppt) cc_final: 0.8744 (mmtm) REVERT: G 58 LYS cc_start: 0.8814 (ttpt) cc_final: 0.7954 (ttpp) REVERT: G 62 GLU cc_start: 0.8063 (pm20) cc_final: 0.7700 (pm20) REVERT: H 18 LYS cc_start: 0.9188 (mppt) cc_final: 0.8982 (mppt) REVERT: B 81 MET cc_start: 0.8239 (tmm) cc_final: 0.7772 (tmm) REVERT: B 655 MET cc_start: 0.8670 (mmm) cc_final: 0.8155 (mmm) REVERT: B 895 MET cc_start: 0.9229 (pmm) cc_final: 0.8926 (pmm) REVERT: B 940 LEU cc_start: 0.9487 (mt) cc_final: 0.9220 (pp) REVERT: B 995 MET cc_start: 0.8820 (ttp) cc_final: 0.8567 (ttm) REVERT: B 2134 MET cc_start: 0.8514 (tpp) cc_final: 0.8200 (tpt) REVERT: B 2585 MET cc_start: 0.7848 (ppp) cc_final: 0.7592 (ppp) REVERT: B 2602 HIS cc_start: 0.8861 (m-70) cc_final: 0.8551 (m-70) REVERT: B 2689 MET cc_start: 0.6486 (mtt) cc_final: 0.6057 (mtp) REVERT: B 2734 MET cc_start: 0.9053 (mmp) cc_final: 0.8726 (mmp) REVERT: B 2837 LEU cc_start: 0.9541 (mt) cc_final: 0.9332 (mt) REVERT: B 2840 MET cc_start: 0.8795 (tpp) cc_final: 0.7890 (tpp) REVERT: B 2843 MET cc_start: 0.9025 (ptt) cc_final: 0.8616 (ppp) REVERT: B 2844 MET cc_start: 0.8865 (ppp) cc_final: 0.8455 (ppp) REVERT: B 2893 LEU cc_start: 0.9595 (mp) cc_final: 0.9301 (mt) REVERT: B 2895 PHE cc_start: 0.8794 (t80) cc_final: 0.8412 (t80) REVERT: B 2897 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8718 (tm-30) REVERT: B 2921 PHE cc_start: 0.8722 (t80) cc_final: 0.8143 (t80) REVERT: B 2932 TYR cc_start: 0.8222 (t80) cc_final: 0.7913 (t80) REVERT: B 2938 GLN cc_start: 0.8924 (pp30) cc_final: 0.8504 (pp30) REVERT: B 2982 PHE cc_start: 0.8756 (m-80) cc_final: 0.8124 (m-80) REVERT: B 3003 MET cc_start: 0.8658 (ptm) cc_final: 0.8230 (ptm) REVERT: B 3022 PHE cc_start: 0.7932 (m-80) cc_final: 0.7652 (m-80) REVERT: B 3031 ASN cc_start: 0.9209 (t0) cc_final: 0.8836 (t0) REVERT: B 3069 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: B 3109 PHE cc_start: 0.9239 (m-10) cc_final: 0.8757 (m-80) REVERT: B 3138 TYR cc_start: 0.9297 (t80) cc_final: 0.8896 (t80) REVERT: B 3152 ARG cc_start: 0.8576 (ptp-170) cc_final: 0.8280 (ptp-170) REVERT: B 3159 LEU cc_start: 0.8853 (pp) cc_final: 0.8001 (pp) REVERT: B 3162 PHE cc_start: 0.8937 (t80) cc_final: 0.8418 (t80) REVERT: B 3241 MET cc_start: 0.9128 (mmp) cc_final: 0.8361 (mmm) REVERT: B 3246 MET cc_start: 0.9110 (mtp) cc_final: 0.8856 (mtm) REVERT: B 3250 TRP cc_start: 0.8838 (t-100) cc_final: 0.8617 (t60) REVERT: B 3302 PHE cc_start: 0.8986 (m-80) cc_final: 0.8704 (m-80) REVERT: B 3304 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8710 (tp-100) REVERT: B 4035 TYR cc_start: 0.8241 (m-80) cc_final: 0.7831 (t80) REVERT: B 4046 ARG cc_start: 0.8555 (tpm170) cc_final: 0.8189 (tpp-160) REVERT: B 4258 MET cc_start: 0.8656 (mtp) cc_final: 0.8135 (ptt) REVERT: B 4707 MET cc_start: 0.8595 (ttp) cc_final: 0.8336 (ttt) REVERT: B 4726 MET cc_start: 0.8383 (tpt) cc_final: 0.7763 (tpp) REVERT: C 81 MET cc_start: 0.8269 (tmm) cc_final: 0.7794 (tmm) REVERT: C 655 MET cc_start: 0.8699 (mmm) cc_final: 0.8203 (mmm) REVERT: C 895 MET cc_start: 0.9221 (pmm) cc_final: 0.8915 (pmm) REVERT: C 940 LEU cc_start: 0.9488 (mt) cc_final: 0.9233 (pp) REVERT: C 995 MET cc_start: 0.8815 (ttp) cc_final: 0.8562 (ttm) REVERT: C 2485 LEU cc_start: 0.9427 (mm) cc_final: 0.9201 (mm) REVERT: C 2666 LEU cc_start: 0.9546 (tt) cc_final: 0.9342 (pp) REVERT: C 2734 MET cc_start: 0.9052 (mmp) cc_final: 0.8675 (mmp) REVERT: C 2782 MET cc_start: 0.8715 (tpt) cc_final: 0.8450 (tpp) REVERT: C 2840 MET cc_start: 0.8583 (tpp) cc_final: 0.8061 (mmt) REVERT: C 2843 MET cc_start: 0.8897 (ptt) cc_final: 0.8470 (ppp) REVERT: C 2844 MET cc_start: 0.8901 (ppp) cc_final: 0.8405 (ppp) REVERT: C 2895 PHE cc_start: 0.8802 (t80) cc_final: 0.8492 (t80) REVERT: C 2897 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8765 (tm-30) REVERT: C 2921 PHE cc_start: 0.8713 (t80) cc_final: 0.8147 (t80) REVERT: C 2932 TYR cc_start: 0.8216 (t80) cc_final: 0.7905 (t80) REVERT: C 2938 GLN cc_start: 0.8931 (pp30) cc_final: 0.8522 (pp30) REVERT: C 2982 PHE cc_start: 0.8787 (m-80) cc_final: 0.8182 (m-80) REVERT: C 3003 MET cc_start: 0.8699 (ptm) cc_final: 0.8288 (ptm) REVERT: C 3022 PHE cc_start: 0.7940 (m-80) cc_final: 0.7644 (m-80) REVERT: C 3031 ASN cc_start: 0.9195 (t0) cc_final: 0.8818 (t0) REVERT: C 3069 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: C 3109 PHE cc_start: 0.9237 (m-10) cc_final: 0.8933 (m-10) REVERT: C 3138 TYR cc_start: 0.9303 (t80) cc_final: 0.8904 (t80) REVERT: C 3152 ARG cc_start: 0.8521 (ptp-170) cc_final: 0.8213 (ptp-170) REVERT: C 3159 LEU cc_start: 0.8858 (pp) cc_final: 0.8283 (pp) REVERT: C 3162 PHE cc_start: 0.8950 (t80) cc_final: 0.8570 (t80) REVERT: C 3241 MET cc_start: 0.9121 (mmp) cc_final: 0.8404 (mmm) REVERT: C 3246 MET cc_start: 0.9111 (mtp) cc_final: 0.8876 (mtm) REVERT: C 3302 PHE cc_start: 0.8989 (m-80) cc_final: 0.8700 (m-80) REVERT: C 3304 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8698 (tp-100) REVERT: C 4035 TYR cc_start: 0.8206 (m-80) cc_final: 0.7772 (t80) REVERT: C 4046 ARG cc_start: 0.8551 (tpm170) cc_final: 0.8144 (tpp-160) REVERT: C 4258 MET cc_start: 0.8665 (mtp) cc_final: 0.8127 (ptt) REVERT: C 4698 LEU cc_start: 0.8584 (mt) cc_final: 0.8366 (mt) REVERT: C 4707 MET cc_start: 0.8599 (ttp) cc_final: 0.8347 (ttt) REVERT: C 4726 MET cc_start: 0.8393 (tpt) cc_final: 0.7829 (tpp) REVERT: D 81 MET cc_start: 0.8266 (tmm) cc_final: 0.7802 (tmm) REVERT: D 655 MET cc_start: 0.8693 (mmm) cc_final: 0.8182 (mmm) REVERT: D 895 MET cc_start: 0.9238 (pmm) cc_final: 0.8938 (pmm) REVERT: D 940 LEU cc_start: 0.9488 (mt) cc_final: 0.9242 (pp) REVERT: D 995 MET cc_start: 0.8801 (ttp) cc_final: 0.8545 (ttm) REVERT: D 2485 LEU cc_start: 0.9429 (mm) cc_final: 0.9200 (mm) REVERT: D 2734 MET cc_start: 0.9037 (mmp) cc_final: 0.8707 (mmp) REVERT: D 2782 MET cc_start: 0.8624 (tpt) cc_final: 0.8301 (tpp) REVERT: D 2840 MET cc_start: 0.8509 (tpp) cc_final: 0.8126 (mmt) REVERT: D 2843 MET cc_start: 0.8916 (ptt) cc_final: 0.8496 (ppp) REVERT: D 2844 MET cc_start: 0.8844 (ppp) cc_final: 0.8347 (ppp) REVERT: D 2893 LEU cc_start: 0.9544 (mt) cc_final: 0.9330 (mt) REVERT: D 2895 PHE cc_start: 0.8826 (t80) cc_final: 0.8520 (t80) REVERT: D 2897 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8813 (tm-30) REVERT: D 2921 PHE cc_start: 0.8716 (t80) cc_final: 0.8136 (t80) REVERT: D 2932 TYR cc_start: 0.8222 (t80) cc_final: 0.7917 (t80) REVERT: D 2938 GLN cc_start: 0.8916 (pp30) cc_final: 0.8519 (pp30) REVERT: D 2982 PHE cc_start: 0.8762 (m-80) cc_final: 0.8124 (m-80) REVERT: D 3003 MET cc_start: 0.8646 (ptm) cc_final: 0.8234 (ptm) REVERT: D 3031 ASN cc_start: 0.9198 (t0) cc_final: 0.8825 (t0) REVERT: D 3069 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: D 3109 PHE cc_start: 0.9240 (m-10) cc_final: 0.8759 (m-80) REVERT: D 3138 TYR cc_start: 0.9311 (t80) cc_final: 0.8934 (t80) REVERT: D 3152 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.8269 (ptp-170) REVERT: D 3159 LEU cc_start: 0.8847 (pp) cc_final: 0.7810 (pp) REVERT: D 3162 PHE cc_start: 0.8955 (t80) cc_final: 0.8436 (t80) REVERT: D 3241 MET cc_start: 0.9128 (mmp) cc_final: 0.8389 (mmt) REVERT: D 3246 MET cc_start: 0.9118 (mtp) cc_final: 0.8883 (mtm) REVERT: D 3250 TRP cc_start: 0.8836 (t-100) cc_final: 0.8613 (t60) REVERT: D 3302 PHE cc_start: 0.8988 (m-80) cc_final: 0.8689 (m-80) REVERT: D 3304 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8706 (tp-100) REVERT: D 4035 TYR cc_start: 0.8247 (m-80) cc_final: 0.7780 (t80) REVERT: D 4046 ARG cc_start: 0.8563 (tpm170) cc_final: 0.8138 (tpp-160) REVERT: D 4258 MET cc_start: 0.8683 (mtp) cc_final: 0.8139 (ptt) REVERT: D 4698 LEU cc_start: 0.8586 (mt) cc_final: 0.8360 (mt) REVERT: D 4707 MET cc_start: 0.8609 (ttp) cc_final: 0.8364 (ttt) REVERT: D 4726 MET cc_start: 0.8400 (tpt) cc_final: 0.7763 (tpp) outliers start: 68 outliers final: 29 residues processed: 1101 average time/residue: 1.1747 time to fit residues: 2283.7287 Evaluate side-chains 1055 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1021 time to evaluate : 11.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 3053 VAL Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 3053 VAL Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 4279 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 20.0000 chunk 1181 optimal weight: 9.9990 chunk 815 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 750 optimal weight: 20.0000 chunk 1055 optimal weight: 1.9990 chunk 1577 optimal weight: 7.9990 chunk 1670 optimal weight: 3.9990 chunk 824 optimal weight: 8.9990 chunk 1495 optimal weight: 7.9990 chunk 450 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 HIS ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2978 HIS ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN B 506 HIS B 949 HIS ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3775 GLN B3955 GLN B3975 GLN ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 HIS ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN D 949 HIS ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4489 GLN ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 141728 Z= 0.422 Angle : 0.678 17.701 191492 Z= 0.338 Chirality : 0.043 0.197 20988 Planarity : 0.005 0.139 24600 Dihedral : 5.819 71.732 19108 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 0.53 % Allowed : 6.88 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.06), residues: 17212 helix: 1.60 (0.06), residues: 8920 sheet: 0.10 (0.13), residues: 1568 loop : -0.44 (0.08), residues: 6724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 893 HIS 0.027 0.001 HIS C3034 PHE 0.055 0.002 PHE C2943 TYR 0.026 0.002 TYR B3245 ARG 0.008 0.001 ARG H 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 1190 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1109 time to evaluate : 11.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8316 (tmm) cc_final: 0.7867 (tmm) REVERT: A 655 MET cc_start: 0.8739 (mmm) cc_final: 0.8199 (mmm) REVERT: A 895 MET cc_start: 0.9258 (pmm) cc_final: 0.8986 (pmm) REVERT: A 995 MET cc_start: 0.8830 (ttp) cc_final: 0.8573 (ttm) REVERT: A 2602 HIS cc_start: 0.8916 (m-70) cc_final: 0.8604 (m-70) REVERT: A 2610 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9131 (mm) REVERT: A 2734 MET cc_start: 0.9091 (mmp) cc_final: 0.8818 (mmp) REVERT: A 2779 LEU cc_start: 0.9421 (mp) cc_final: 0.8996 (pt) REVERT: A 2782 MET cc_start: 0.8718 (tpt) cc_final: 0.8394 (tpp) REVERT: A 2833 LEU cc_start: 0.8969 (mt) cc_final: 0.8687 (mt) REVERT: A 2844 MET cc_start: 0.8884 (ppp) cc_final: 0.8551 (ppp) REVERT: A 2848 TYR cc_start: 0.8873 (m-10) cc_final: 0.8605 (m-80) REVERT: A 2887 GLU cc_start: 0.8900 (pp20) cc_final: 0.8647 (pp20) REVERT: A 2893 LEU cc_start: 0.9616 (mt) cc_final: 0.9291 (tt) REVERT: A 2895 PHE cc_start: 0.8934 (t80) cc_final: 0.8532 (t80) REVERT: A 2897 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 2921 PHE cc_start: 0.8768 (t80) cc_final: 0.8397 (t80) REVERT: A 2926 LEU cc_start: 0.9648 (mt) cc_final: 0.9253 (tp) REVERT: A 2932 TYR cc_start: 0.8305 (t80) cc_final: 0.7977 (t80) REVERT: A 2938 GLN cc_start: 0.8937 (pp30) cc_final: 0.8517 (pp30) REVERT: A 2943 PHE cc_start: 0.7921 (m-80) cc_final: 0.7695 (m-80) REVERT: A 2975 PHE cc_start: 0.8918 (m-80) cc_final: 0.8491 (m-10) REVERT: A 2982 PHE cc_start: 0.8848 (m-80) cc_final: 0.8186 (m-80) REVERT: A 3003 MET cc_start: 0.8671 (ptm) cc_final: 0.8374 (ptm) REVERT: A 3022 PHE cc_start: 0.8029 (m-80) cc_final: 0.7730 (m-80) REVERT: A 3031 ASN cc_start: 0.9213 (t0) cc_final: 0.8836 (t0) REVERT: A 3068 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8892 (pt) REVERT: A 3069 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: A 3105 LEU cc_start: 0.9007 (mm) cc_final: 0.8523 (tt) REVERT: A 3109 PHE cc_start: 0.9313 (m-10) cc_final: 0.8948 (m-80) REVERT: A 3138 TYR cc_start: 0.9328 (t80) cc_final: 0.8928 (t80) REVERT: A 3152 ARG cc_start: 0.8689 (ptp-170) cc_final: 0.8153 (ptp-110) REVERT: A 3159 LEU cc_start: 0.8879 (pp) cc_final: 0.7824 (pp) REVERT: A 3166 PHE cc_start: 0.9040 (t80) cc_final: 0.7872 (t80) REVERT: A 3241 MET cc_start: 0.9230 (mmp) cc_final: 0.8403 (mmm) REVERT: A 3246 MET cc_start: 0.9132 (mtp) cc_final: 0.8739 (mmm) REVERT: A 3248 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8234 (ttt180) REVERT: A 3302 PHE cc_start: 0.9006 (m-80) cc_final: 0.8703 (m-80) REVERT: A 3304 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8615 (tp-100) REVERT: A 4707 MET cc_start: 0.8629 (ttp) cc_final: 0.8379 (ttt) REVERT: A 4726 MET cc_start: 0.8409 (tpt) cc_final: 0.7675 (tpp) REVERT: E 4 GLU cc_start: 0.7735 (mp0) cc_final: 0.7459 (mp0) REVERT: E 18 LYS cc_start: 0.9171 (mppt) cc_final: 0.8915 (mppt) REVERT: E 81 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9237 (p) REVERT: F 18 LYS cc_start: 0.8930 (mppt) cc_final: 0.8595 (mppt) REVERT: F 62 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: F 81 VAL cc_start: 0.9476 (OUTLIER) cc_final: 0.9223 (p) REVERT: G 4 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7508 (mp0) REVERT: G 18 LYS cc_start: 0.9081 (mppt) cc_final: 0.8863 (mmtm) REVERT: H 18 LYS cc_start: 0.9194 (mppt) cc_final: 0.8961 (mppt) REVERT: H 81 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9250 (p) REVERT: B 81 MET cc_start: 0.8279 (tmm) cc_final: 0.7816 (tmm) REVERT: B 655 MET cc_start: 0.8757 (mmm) cc_final: 0.8161 (mmm) REVERT: B 895 MET cc_start: 0.9277 (pmm) cc_final: 0.9012 (pmm) REVERT: B 995 MET cc_start: 0.8831 (ttp) cc_final: 0.8580 (ttm) REVERT: B 2485 LEU cc_start: 0.9444 (mm) cc_final: 0.9205 (mm) REVERT: B 2585 MET cc_start: 0.7932 (ppp) cc_final: 0.7679 (ppp) REVERT: B 2602 HIS cc_start: 0.8921 (m-70) cc_final: 0.8615 (m-70) REVERT: B 2666 LEU cc_start: 0.9475 (pp) cc_final: 0.9258 (pt) REVERT: B 2689 MET cc_start: 0.6481 (mtt) cc_final: 0.5920 (mtp) REVERT: B 2734 MET cc_start: 0.9060 (mmp) cc_final: 0.8732 (mmp) REVERT: B 2837 LEU cc_start: 0.9564 (mt) cc_final: 0.9346 (mt) REVERT: B 2840 MET cc_start: 0.8893 (tpp) cc_final: 0.7911 (tpp) REVERT: B 2843 MET cc_start: 0.9111 (ptt) cc_final: 0.8703 (ppp) REVERT: B 2844 MET cc_start: 0.8916 (ppp) cc_final: 0.8548 (ppp) REVERT: B 2893 LEU cc_start: 0.9589 (mp) cc_final: 0.9288 (mt) REVERT: B 2895 PHE cc_start: 0.8883 (t80) cc_final: 0.8489 (t80) REVERT: B 2897 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8756 (tm-30) REVERT: B 2921 PHE cc_start: 0.8773 (t80) cc_final: 0.8396 (t80) REVERT: B 2926 LEU cc_start: 0.9640 (mt) cc_final: 0.9254 (tp) REVERT: B 2932 TYR cc_start: 0.8296 (t80) cc_final: 0.7926 (t80) REVERT: B 2938 GLN cc_start: 0.8994 (pp30) cc_final: 0.8605 (pp30) REVERT: B 2963 PHE cc_start: 0.9136 (t80) cc_final: 0.8838 (t80) REVERT: B 2975 PHE cc_start: 0.8930 (m-80) cc_final: 0.8482 (m-10) REVERT: B 2982 PHE cc_start: 0.8812 (m-80) cc_final: 0.8133 (m-80) REVERT: B 3003 MET cc_start: 0.8679 (ptm) cc_final: 0.8371 (ptm) REVERT: B 3022 PHE cc_start: 0.8049 (m-80) cc_final: 0.7709 (m-80) REVERT: B 3031 ASN cc_start: 0.9224 (t0) cc_final: 0.8852 (t0) REVERT: B 3068 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8923 (pt) REVERT: B 3069 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8390 (mm-30) REVERT: B 3138 TYR cc_start: 0.9329 (t80) cc_final: 0.8955 (t80) REVERT: B 3152 ARG cc_start: 0.8695 (ptp-170) cc_final: 0.8116 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8856 (pp) cc_final: 0.7662 (pp) REVERT: B 3162 PHE cc_start: 0.8997 (t80) cc_final: 0.8727 (t80) REVERT: B 3241 MET cc_start: 0.9205 (mmp) cc_final: 0.8429 (mmt) REVERT: B 3246 MET cc_start: 0.9157 (mtp) cc_final: 0.8750 (mmm) REVERT: B 3250 TRP cc_start: 0.8788 (t-100) cc_final: 0.8572 (t60) REVERT: B 3302 PHE cc_start: 0.8999 (m-80) cc_final: 0.8711 (m-80) REVERT: B 3304 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8703 (tp-100) REVERT: B 4274 MET cc_start: 0.4830 (ttm) cc_final: 0.3969 (mtp) REVERT: B 4707 MET cc_start: 0.8621 (ttp) cc_final: 0.8359 (ttt) REVERT: B 4726 MET cc_start: 0.8396 (tpt) cc_final: 0.7657 (tpp) REVERT: C 81 MET cc_start: 0.8316 (tmm) cc_final: 0.7851 (tmm) REVERT: C 655 MET cc_start: 0.8802 (mmm) cc_final: 0.8199 (mmm) REVERT: C 895 MET cc_start: 0.9275 (pmm) cc_final: 0.9002 (pmm) REVERT: C 940 LEU cc_start: 0.9495 (mt) cc_final: 0.9250 (pp) REVERT: C 995 MET cc_start: 0.8840 (ttp) cc_final: 0.8586 (ttm) REVERT: C 2485 LEU cc_start: 0.9446 (mm) cc_final: 0.9212 (mm) REVERT: C 2585 MET cc_start: 0.8465 (ppp) cc_final: 0.7988 (ppp) REVERT: C 2602 HIS cc_start: 0.8914 (m-70) cc_final: 0.8599 (m-70) REVERT: C 2689 MET cc_start: 0.6869 (mtt) cc_final: 0.6545 (ptp) REVERT: C 2734 MET cc_start: 0.9081 (mmp) cc_final: 0.8750 (mmp) REVERT: C 2782 MET cc_start: 0.8792 (tpt) cc_final: 0.8567 (tpp) REVERT: C 2840 MET cc_start: 0.8560 (tpp) cc_final: 0.8010 (mmt) REVERT: C 2843 MET cc_start: 0.8929 (ptt) cc_final: 0.8538 (ppp) REVERT: C 2844 MET cc_start: 0.8911 (ppp) cc_final: 0.8384 (ppp) REVERT: C 2895 PHE cc_start: 0.8921 (t80) cc_final: 0.8512 (t80) REVERT: C 2897 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 2932 TYR cc_start: 0.8266 (t80) cc_final: 0.7905 (t80) REVERT: C 2938 GLN cc_start: 0.8954 (pp30) cc_final: 0.8563 (pp30) REVERT: C 2963 PHE cc_start: 0.9170 (t80) cc_final: 0.8869 (t80) REVERT: C 2975 PHE cc_start: 0.8923 (m-80) cc_final: 0.8509 (m-10) REVERT: C 2982 PHE cc_start: 0.8851 (m-80) cc_final: 0.8280 (m-80) REVERT: C 3003 MET cc_start: 0.8722 (ptm) cc_final: 0.8326 (ptm) REVERT: C 3022 PHE cc_start: 0.8025 (m-80) cc_final: 0.7711 (m-80) REVERT: C 3031 ASN cc_start: 0.9206 (t0) cc_final: 0.8840 (t0) REVERT: C 3068 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8948 (pt) REVERT: C 3069 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: C 3138 TYR cc_start: 0.9336 (t80) cc_final: 0.8972 (t80) REVERT: C 3152 ARG cc_start: 0.8672 (ptp-170) cc_final: 0.8108 (ptp-110) REVERT: C 3159 LEU cc_start: 0.8868 (pp) cc_final: 0.7701 (pp) REVERT: C 3162 PHE cc_start: 0.9007 (t80) cc_final: 0.8717 (t80) REVERT: C 3241 MET cc_start: 0.9182 (mmp) cc_final: 0.8411 (mmt) REVERT: C 3246 MET cc_start: 0.9072 (mtp) cc_final: 0.8834 (mtm) REVERT: C 3248 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8310 (ttt180) REVERT: C 3302 PHE cc_start: 0.9020 (m-80) cc_final: 0.8722 (m-80) REVERT: C 3304 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8626 (tp-100) REVERT: C 4258 MET cc_start: 0.8655 (mtp) cc_final: 0.8132 (ptt) REVERT: C 4274 MET cc_start: 0.4777 (ttm) cc_final: 0.3901 (mtp) REVERT: C 4698 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8364 (mt) REVERT: C 4707 MET cc_start: 0.8638 (ttp) cc_final: 0.8387 (ttt) REVERT: C 4726 MET cc_start: 0.8387 (tpt) cc_final: 0.7660 (tpp) REVERT: D 81 MET cc_start: 0.8285 (tmm) cc_final: 0.7822 (tmm) REVERT: D 655 MET cc_start: 0.8781 (mmm) cc_final: 0.8207 (mmm) REVERT: D 895 MET cc_start: 0.9289 (pmm) cc_final: 0.9030 (pmm) REVERT: D 940 LEU cc_start: 0.9498 (mt) cc_final: 0.9255 (pp) REVERT: D 995 MET cc_start: 0.8847 (ttp) cc_final: 0.8591 (ttm) REVERT: D 2485 LEU cc_start: 0.9452 (mm) cc_final: 0.9211 (mm) REVERT: D 2602 HIS cc_start: 0.8907 (m-70) cc_final: 0.8604 (m-70) REVERT: D 2666 LEU cc_start: 0.9485 (pp) cc_final: 0.9266 (pt) REVERT: D 2689 MET cc_start: 0.6831 (mtt) cc_final: 0.6618 (ptp) REVERT: D 2734 MET cc_start: 0.9037 (mmp) cc_final: 0.8700 (mmp) REVERT: D 2779 LEU cc_start: 0.9527 (mp) cc_final: 0.9105 (pt) REVERT: D 2782 MET cc_start: 0.8748 (tpt) cc_final: 0.8511 (tpp) REVERT: D 2843 MET cc_start: 0.8933 (ptt) cc_final: 0.8641 (ppp) REVERT: D 2844 MET cc_start: 0.8873 (ppp) cc_final: 0.8424 (ppp) REVERT: D 2893 LEU cc_start: 0.9566 (mt) cc_final: 0.9308 (tt) REVERT: D 2895 PHE cc_start: 0.8934 (t80) cc_final: 0.8581 (t80) REVERT: D 2897 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8828 (tm-30) REVERT: D 2921 PHE cc_start: 0.8782 (t80) cc_final: 0.8410 (t80) REVERT: D 2932 TYR cc_start: 0.8273 (t80) cc_final: 0.7916 (t80) REVERT: D 2938 GLN cc_start: 0.8956 (pp30) cc_final: 0.8549 (pp30) REVERT: D 2963 PHE cc_start: 0.9135 (t80) cc_final: 0.8839 (t80) REVERT: D 2975 PHE cc_start: 0.8943 (m-80) cc_final: 0.8517 (m-10) REVERT: D 2982 PHE cc_start: 0.8820 (m-80) cc_final: 0.8203 (m-80) REVERT: D 3003 MET cc_start: 0.8672 (ptm) cc_final: 0.8261 (ptm) REVERT: D 3031 ASN cc_start: 0.9215 (t0) cc_final: 0.8834 (t0) REVERT: D 3068 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8982 (pt) REVERT: D 3069 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: D 3138 TYR cc_start: 0.9346 (t80) cc_final: 0.8991 (t80) REVERT: D 3152 ARG cc_start: 0.8692 (ptp-170) cc_final: 0.8111 (ptp-110) REVERT: D 3159 LEU cc_start: 0.8860 (pp) cc_final: 0.7754 (pp) REVERT: D 3162 PHE cc_start: 0.9000 (t80) cc_final: 0.8722 (t80) REVERT: D 3166 PHE cc_start: 0.9009 (t80) cc_final: 0.7994 (t80) REVERT: D 3241 MET cc_start: 0.9200 (mmp) cc_final: 0.8391 (mmt) REVERT: D 3246 MET cc_start: 0.9131 (mtp) cc_final: 0.8927 (mtm) REVERT: D 3248 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8333 (ttt180) REVERT: D 3302 PHE cc_start: 0.9025 (m-80) cc_final: 0.8711 (m-80) REVERT: D 3304 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8696 (tp-100) REVERT: D 4258 MET cc_start: 0.8691 (mtp) cc_final: 0.8168 (ptt) REVERT: D 4274 MET cc_start: 0.4778 (ttm) cc_final: 0.3927 (mtp) REVERT: D 4698 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8370 (mt) REVERT: D 4707 MET cc_start: 0.8673 (ttp) cc_final: 0.8318 (ttp) REVERT: D 4726 MET cc_start: 0.8409 (tpt) cc_final: 0.7682 (tpp) REVERT: D 4804 MET cc_start: 0.9012 (mmp) cc_final: 0.8694 (mmm) outliers start: 81 outliers final: 54 residues processed: 1141 average time/residue: 1.1794 time to fit residues: 2379.4075 Evaluate side-chains 1141 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1072 time to evaluate : 11.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 2172 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3053 VAL Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1628 MET Chi-restraints excluded: chain C residue 2172 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3053 VAL Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 2172 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2980 LEU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 40.0000 chunk 948 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 1243 optimal weight: 0.9990 chunk 689 optimal weight: 20.0000 chunk 1425 optimal weight: 0.3980 chunk 1154 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 852 optimal weight: 1.9990 chunk 1499 optimal weight: 9.9990 chunk 421 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN A2704 GLN ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4961 GLN F 21 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 GLN B2579 GLN B2739 ASN ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** B4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4961 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 GLN C2541 HIS C2579 GLN ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN D2541 HIS D2579 GLN ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3905 ASN D3955 GLN D3975 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 141728 Z= 0.275 Angle : 0.640 18.183 191492 Z= 0.315 Chirality : 0.041 0.228 20988 Planarity : 0.004 0.135 24600 Dihedral : 5.624 68.422 19108 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 0.66 % Allowed : 7.44 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.06), residues: 17212 helix: 1.69 (0.06), residues: 8868 sheet: 0.05 (0.13), residues: 1604 loop : -0.37 (0.08), residues: 6740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 893 HIS 0.025 0.001 HIS C3034 PHE 0.045 0.001 PHE B2943 TYR 0.042 0.001 TYR B3245 ARG 0.009 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1079 time to evaluate : 12.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8310 (tmm) cc_final: 0.7849 (tmm) REVERT: A 535 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 655 MET cc_start: 0.8689 (mmm) cc_final: 0.8113 (mmm) REVERT: A 895 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8531 (ptp) REVERT: A 995 MET cc_start: 0.8819 (ttp) cc_final: 0.8568 (ttm) REVERT: A 2610 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9092 (mm) REVERT: A 2734 MET cc_start: 0.9079 (mmp) cc_final: 0.8796 (mmp) REVERT: A 2833 LEU cc_start: 0.8966 (mt) cc_final: 0.8684 (mt) REVERT: A 2840 MET cc_start: 0.9050 (mmt) cc_final: 0.8712 (mmt) REVERT: A 2844 MET cc_start: 0.8855 (ppp) cc_final: 0.8568 (ppp) REVERT: A 2848 TYR cc_start: 0.8901 (m-10) cc_final: 0.8647 (m-80) REVERT: A 2887 GLU cc_start: 0.8874 (pp20) cc_final: 0.8603 (pp20) REVERT: A 2890 GLN cc_start: 0.8884 (mp10) cc_final: 0.8418 (mt0) REVERT: A 2893 LEU cc_start: 0.9594 (mt) cc_final: 0.9253 (tt) REVERT: A 2895 PHE cc_start: 0.8953 (t80) cc_final: 0.8614 (t80) REVERT: A 2897 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 2921 PHE cc_start: 0.8716 (t80) cc_final: 0.8284 (t80) REVERT: A 2932 TYR cc_start: 0.8262 (t80) cc_final: 0.7951 (t80) REVERT: A 2938 GLN cc_start: 0.8955 (pp30) cc_final: 0.8548 (pp30) REVERT: A 2975 PHE cc_start: 0.8929 (m-80) cc_final: 0.8477 (m-10) REVERT: A 2982 PHE cc_start: 0.8805 (m-80) cc_final: 0.8200 (m-80) REVERT: A 3003 MET cc_start: 0.8612 (ptm) cc_final: 0.8232 (ptm) REVERT: A 3022 PHE cc_start: 0.7987 (m-80) cc_final: 0.7700 (m-80) REVERT: A 3031 ASN cc_start: 0.9214 (t0) cc_final: 0.8828 (t0) REVERT: A 3040 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7224 (mt) REVERT: A 3068 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8914 (pt) REVERT: A 3069 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: A 3105 LEU cc_start: 0.9027 (mm) cc_final: 0.8476 (tt) REVERT: A 3109 PHE cc_start: 0.9320 (m-10) cc_final: 0.8890 (m-80) REVERT: A 3138 TYR cc_start: 0.9326 (t80) cc_final: 0.8926 (t80) REVERT: A 3152 ARG cc_start: 0.8722 (ptp-170) cc_final: 0.8159 (ptp-110) REVERT: A 3159 LEU cc_start: 0.8878 (pp) cc_final: 0.7630 (pp) REVERT: A 3162 PHE cc_start: 0.8935 (t80) cc_final: 0.8714 (t80) REVERT: A 3241 MET cc_start: 0.9219 (mmp) cc_final: 0.8454 (mmt) REVERT: A 3246 MET cc_start: 0.9069 (mtp) cc_final: 0.8706 (mmm) REVERT: A 3249 TRP cc_start: 0.8792 (m100) cc_final: 0.8544 (m100) REVERT: A 3302 PHE cc_start: 0.8968 (m-80) cc_final: 0.8677 (m-80) REVERT: A 3304 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8569 (tp-100) REVERT: A 4035 TYR cc_start: 0.8205 (m-80) cc_final: 0.7805 (t80) REVERT: A 4046 ARG cc_start: 0.8517 (tpm170) cc_final: 0.8004 (tpm170) REVERT: A 4274 MET cc_start: 0.4900 (ttm) cc_final: 0.4074 (mtp) REVERT: A 4672 MET cc_start: 0.8591 (mtm) cc_final: 0.8372 (mtm) REVERT: A 4707 MET cc_start: 0.8592 (ttp) cc_final: 0.8337 (ttt) REVERT: A 4726 MET cc_start: 0.8378 (tpt) cc_final: 0.7674 (tpp) REVERT: E 4 GLU cc_start: 0.7709 (mp0) cc_final: 0.7478 (mp0) REVERT: E 18 LYS cc_start: 0.9157 (mppt) cc_final: 0.8907 (mppt) REVERT: F 18 LYS cc_start: 0.8887 (mppt) cc_final: 0.8541 (mppt) REVERT: F 58 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8071 (ttpp) REVERT: F 62 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: G 4 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7482 (mp0) REVERT: G 18 LYS cc_start: 0.9131 (mppt) cc_final: 0.8896 (mmtm) REVERT: H 81 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9206 (p) REVERT: B 81 MET cc_start: 0.8282 (tmm) cc_final: 0.7803 (tmm) REVERT: B 655 MET cc_start: 0.8710 (mmm) cc_final: 0.8125 (mmm) REVERT: B 895 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9042 (pmm) REVERT: B 940 LEU cc_start: 0.9491 (mt) cc_final: 0.9243 (pp) REVERT: B 995 MET cc_start: 0.8825 (ttp) cc_final: 0.8570 (ttm) REVERT: B 2485 LEU cc_start: 0.9429 (mm) cc_final: 0.9184 (mm) REVERT: B 2585 MET cc_start: 0.7863 (ppp) cc_final: 0.7589 (ppp) REVERT: B 2666 LEU cc_start: 0.9498 (pp) cc_final: 0.9273 (pt) REVERT: B 2689 MET cc_start: 0.6385 (mtt) cc_final: 0.5840 (mtp) REVERT: B 2734 MET cc_start: 0.9068 (mmp) cc_final: 0.8774 (mmp) REVERT: B 2779 LEU cc_start: 0.9438 (mp) cc_final: 0.9117 (pt) REVERT: B 2837 LEU cc_start: 0.9558 (mt) cc_final: 0.9347 (mt) REVERT: B 2840 MET cc_start: 0.8889 (tpp) cc_final: 0.8216 (tpp) REVERT: B 2843 MET cc_start: 0.9084 (ptt) cc_final: 0.8659 (ppp) REVERT: B 2844 MET cc_start: 0.8923 (ppp) cc_final: 0.8472 (ppp) REVERT: B 2893 LEU cc_start: 0.9574 (mp) cc_final: 0.9336 (mt) REVERT: B 2895 PHE cc_start: 0.8973 (t80) cc_final: 0.8684 (t80) REVERT: B 2897 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 2921 PHE cc_start: 0.8722 (t80) cc_final: 0.8298 (t80) REVERT: B 2926 LEU cc_start: 0.9628 (mt) cc_final: 0.9278 (tp) REVERT: B 2932 TYR cc_start: 0.8252 (t80) cc_final: 0.7919 (t80) REVERT: B 2938 GLN cc_start: 0.8956 (pp30) cc_final: 0.8516 (pp30) REVERT: B 2975 PHE cc_start: 0.8921 (m-80) cc_final: 0.8426 (m-10) REVERT: B 2982 PHE cc_start: 0.8781 (m-80) cc_final: 0.8093 (m-80) REVERT: B 3003 MET cc_start: 0.8631 (ptm) cc_final: 0.8317 (ptm) REVERT: B 3022 PHE cc_start: 0.7994 (m-80) cc_final: 0.7684 (m-80) REVERT: B 3031 ASN cc_start: 0.9217 (t0) cc_final: 0.8824 (t0) REVERT: B 3040 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7463 (mt) REVERT: B 3068 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8949 (pt) REVERT: B 3069 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: B 3138 TYR cc_start: 0.9329 (t80) cc_final: 0.8958 (t80) REVERT: B 3152 ARG cc_start: 0.8748 (ptp-170) cc_final: 0.8157 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8848 (pp) cc_final: 0.7643 (pp) REVERT: B 3162 PHE cc_start: 0.8973 (t80) cc_final: 0.8724 (t80) REVERT: B 3241 MET cc_start: 0.9216 (mmp) cc_final: 0.8411 (mmt) REVERT: B 3246 MET cc_start: 0.9101 (mtp) cc_final: 0.8868 (mtm) REVERT: B 3302 PHE cc_start: 0.8967 (m-80) cc_final: 0.8745 (m-80) REVERT: B 3304 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8629 (tp-100) REVERT: B 4035 TYR cc_start: 0.8214 (m-80) cc_final: 0.7767 (t80) REVERT: B 4046 ARG cc_start: 0.8570 (tpm170) cc_final: 0.8055 (tpm170) REVERT: B 4274 MET cc_start: 0.4772 (ttm) cc_final: 0.3845 (mtp) REVERT: B 4672 MET cc_start: 0.8762 (mtm) cc_final: 0.8406 (mtm) REVERT: B 4707 MET cc_start: 0.8603 (ttp) cc_final: 0.8348 (ttt) REVERT: B 4726 MET cc_start: 0.8369 (tpt) cc_final: 0.7646 (tpp) REVERT: C 81 MET cc_start: 0.8306 (tmm) cc_final: 0.7824 (tmm) REVERT: C 655 MET cc_start: 0.8731 (mmm) cc_final: 0.8136 (mmm) REVERT: C 895 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9035 (pmm) REVERT: C 940 LEU cc_start: 0.9486 (mt) cc_final: 0.9252 (pp) REVERT: C 995 MET cc_start: 0.8823 (ttp) cc_final: 0.8568 (ttm) REVERT: C 2485 LEU cc_start: 0.9430 (mm) cc_final: 0.9190 (mm) REVERT: C 2585 MET cc_start: 0.8363 (ppp) cc_final: 0.7958 (ppp) REVERT: C 2689 MET cc_start: 0.6818 (mtt) cc_final: 0.6393 (mtp) REVERT: C 2734 MET cc_start: 0.9056 (mmp) cc_final: 0.8705 (mmp) REVERT: C 2779 LEU cc_start: 0.9491 (mp) cc_final: 0.9210 (pt) REVERT: C 2844 MET cc_start: 0.8890 (ppp) cc_final: 0.8612 (ppp) REVERT: C 2895 PHE cc_start: 0.8934 (t80) cc_final: 0.8540 (t80) REVERT: C 2897 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8774 (tm-30) REVERT: C 2921 PHE cc_start: 0.8712 (t80) cc_final: 0.8370 (t80) REVERT: C 2932 TYR cc_start: 0.8219 (t80) cc_final: 0.7899 (t80) REVERT: C 2938 GLN cc_start: 0.8975 (pp30) cc_final: 0.8524 (pp30) REVERT: C 2975 PHE cc_start: 0.8905 (m-80) cc_final: 0.8435 (m-10) REVERT: C 2982 PHE cc_start: 0.8817 (m-80) cc_final: 0.8235 (m-80) REVERT: C 3003 MET cc_start: 0.8714 (ptm) cc_final: 0.8336 (ptm) REVERT: C 3022 PHE cc_start: 0.7981 (m-80) cc_final: 0.7689 (m-80) REVERT: C 3031 ASN cc_start: 0.9203 (t0) cc_final: 0.8809 (t0) REVERT: C 3040 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7431 (mt) REVERT: C 3068 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8938 (pt) REVERT: C 3069 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: C 3138 TYR cc_start: 0.9333 (t80) cc_final: 0.8981 (t80) REVERT: C 3152 ARG cc_start: 0.8726 (ptp-170) cc_final: 0.8414 (ptp-170) REVERT: C 3159 LEU cc_start: 0.8876 (pp) cc_final: 0.7785 (pp) REVERT: C 3162 PHE cc_start: 0.8965 (t80) cc_final: 0.8725 (t80) REVERT: C 3241 MET cc_start: 0.9187 (mmp) cc_final: 0.8395 (mmt) REVERT: C 3246 MET cc_start: 0.9066 (mtp) cc_final: 0.8859 (mtm) REVERT: C 3249 TRP cc_start: 0.8937 (m100) cc_final: 0.8537 (m100) REVERT: C 3302 PHE cc_start: 0.8954 (m-80) cc_final: 0.8730 (m-80) REVERT: C 3304 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8592 (tp-100) REVERT: C 4035 TYR cc_start: 0.8207 (m-80) cc_final: 0.7771 (t80) REVERT: C 4046 ARG cc_start: 0.8556 (tpm170) cc_final: 0.8007 (tpm170) REVERT: C 4274 MET cc_start: 0.4886 (ttm) cc_final: 0.3945 (mtp) REVERT: C 4672 MET cc_start: 0.8587 (mtm) cc_final: 0.8385 (mtm) REVERT: C 4698 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (mt) REVERT: C 4707 MET cc_start: 0.8602 (ttp) cc_final: 0.8344 (ttt) REVERT: D 81 MET cc_start: 0.8289 (tmm) cc_final: 0.7808 (tmm) REVERT: D 655 MET cc_start: 0.8723 (mmm) cc_final: 0.8140 (mmm) REVERT: D 678 MET cc_start: 0.8067 (ttp) cc_final: 0.7754 (ttp) REVERT: D 895 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9049 (pmm) REVERT: D 940 LEU cc_start: 0.9488 (mt) cc_final: 0.9253 (pp) REVERT: D 995 MET cc_start: 0.8834 (ttp) cc_final: 0.8580 (ttm) REVERT: D 2485 LEU cc_start: 0.9435 (mm) cc_final: 0.9213 (mm) REVERT: D 2666 LEU cc_start: 0.9502 (pp) cc_final: 0.9277 (pt) REVERT: D 2689 MET cc_start: 0.6690 (mtt) cc_final: 0.6471 (ptp) REVERT: D 2734 MET cc_start: 0.9045 (mmp) cc_final: 0.8715 (mmp) REVERT: D 2840 MET cc_start: 0.9006 (mmt) cc_final: 0.8752 (mmt) REVERT: D 2844 MET cc_start: 0.8878 (ppp) cc_final: 0.8519 (ppp) REVERT: D 2890 GLN cc_start: 0.8904 (mp10) cc_final: 0.8442 (mt0) REVERT: D 2893 LEU cc_start: 0.9558 (mt) cc_final: 0.9314 (tt) REVERT: D 2895 PHE cc_start: 0.8964 (t80) cc_final: 0.8627 (t80) REVERT: D 2897 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8792 (tm-30) REVERT: D 2921 PHE cc_start: 0.8729 (t80) cc_final: 0.8311 (t80) REVERT: D 2932 TYR cc_start: 0.8229 (t80) cc_final: 0.7919 (t80) REVERT: D 2938 GLN cc_start: 0.8962 (pp30) cc_final: 0.8527 (pp30) REVERT: D 2975 PHE cc_start: 0.8933 (m-80) cc_final: 0.8457 (m-10) REVERT: D 2982 PHE cc_start: 0.8783 (m-80) cc_final: 0.8161 (m-80) REVERT: D 3003 MET cc_start: 0.8645 (ptm) cc_final: 0.8256 (ptm) REVERT: D 3031 ASN cc_start: 0.9217 (t0) cc_final: 0.8819 (t0) REVERT: D 3040 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7476 (mt) REVERT: D 3068 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8937 (pt) REVERT: D 3069 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: D 3138 TYR cc_start: 0.9338 (t80) cc_final: 0.8985 (t80) REVERT: D 3152 ARG cc_start: 0.8717 (ptp-170) cc_final: 0.8132 (ptp-110) REVERT: D 3159 LEU cc_start: 0.8864 (pp) cc_final: 0.7638 (pp) REVERT: D 3162 PHE cc_start: 0.8984 (t80) cc_final: 0.8732 (t80) REVERT: D 3241 MET cc_start: 0.9201 (mmp) cc_final: 0.8391 (mmt) REVERT: D 3249 TRP cc_start: 0.8910 (m100) cc_final: 0.8532 (m100) REVERT: D 3302 PHE cc_start: 0.8971 (m-80) cc_final: 0.8759 (m-80) REVERT: D 3304 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8625 (tp-100) REVERT: D 4035 TYR cc_start: 0.8216 (m-80) cc_final: 0.7777 (t80) REVERT: D 4046 ARG cc_start: 0.8576 (tpm170) cc_final: 0.8006 (tpm170) REVERT: D 4274 MET cc_start: 0.4857 (ttm) cc_final: 0.3945 (mtp) REVERT: D 4698 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8359 (mt) REVERT: D 4707 MET cc_start: 0.8622 (ttp) cc_final: 0.8266 (ttp) REVERT: D 4804 MET cc_start: 0.9031 (mmp) cc_final: 0.8694 (mmm) outliers start: 100 outliers final: 49 residues processed: 1124 average time/residue: 1.1822 time to fit residues: 2342.9949 Evaluate side-chains 1124 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1053 time to evaluate : 10.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3053 VAL Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3686 PHE Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1628 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 30.0000 chunk 1504 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 980 optimal weight: 9.9990 chunk 412 optimal weight: 4.9990 chunk 1671 optimal weight: 5.9990 chunk 1387 optimal weight: 1.9990 chunk 774 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 553 optimal weight: 40.0000 chunk 877 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 GLN B2541 HIS B2739 ASN ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN B3905 ASN B4933 HIS ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 GLN ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 141728 Z= 0.231 Angle : 0.631 18.599 191492 Z= 0.307 Chirality : 0.041 0.238 20988 Planarity : 0.004 0.132 24600 Dihedral : 5.478 69.793 19108 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 0.76 % Allowed : 7.66 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.06), residues: 17212 helix: 1.73 (0.06), residues: 8872 sheet: 0.03 (0.13), residues: 1624 loop : -0.34 (0.08), residues: 6716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C3250 HIS 0.024 0.001 HIS C3034 PHE 0.048 0.001 PHE C2943 TYR 0.029 0.001 TYR B3245 ARG 0.012 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1088 time to evaluate : 13.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8317 (tmm) cc_final: 0.7857 (tmm) REVERT: A 535 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 655 MET cc_start: 0.8653 (mmm) cc_final: 0.8086 (mmm) REVERT: A 890 HIS cc_start: 0.9329 (OUTLIER) cc_final: 0.8873 (p-80) REVERT: A 895 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.9011 (pmm) REVERT: A 995 MET cc_start: 0.8804 (ttp) cc_final: 0.8546 (ttm) REVERT: A 2610 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 2734 MET cc_start: 0.9041 (mmp) cc_final: 0.8809 (mmp) REVERT: A 2779 LEU cc_start: 0.9424 (mp) cc_final: 0.9086 (pt) REVERT: A 2844 MET cc_start: 0.8892 (ppp) cc_final: 0.8599 (ppp) REVERT: A 2848 TYR cc_start: 0.8919 (m-10) cc_final: 0.8678 (m-80) REVERT: A 2887 GLU cc_start: 0.8862 (pp20) cc_final: 0.8633 (pp20) REVERT: A 2895 PHE cc_start: 0.8972 (t80) cc_final: 0.8743 (t80) REVERT: A 2897 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8692 (tm-30) REVERT: A 2921 PHE cc_start: 0.8669 (t80) cc_final: 0.8201 (t80) REVERT: A 2932 TYR cc_start: 0.8277 (t80) cc_final: 0.7975 (t80) REVERT: A 2938 GLN cc_start: 0.8926 (pp30) cc_final: 0.8496 (pp30) REVERT: A 2975 PHE cc_start: 0.8933 (m-80) cc_final: 0.8709 (m-80) REVERT: A 2982 PHE cc_start: 0.8786 (m-80) cc_final: 0.8177 (m-80) REVERT: A 3003 MET cc_start: 0.8574 (ptm) cc_final: 0.8209 (ptm) REVERT: A 3022 PHE cc_start: 0.8031 (m-80) cc_final: 0.7694 (m-80) REVERT: A 3031 ASN cc_start: 0.9199 (t0) cc_final: 0.8789 (t0) REVERT: A 3040 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7217 (mt) REVERT: A 3068 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8900 (pt) REVERT: A 3069 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: A 3105 LEU cc_start: 0.9038 (mm) cc_final: 0.8496 (tt) REVERT: A 3109 PHE cc_start: 0.9325 (m-10) cc_final: 0.8927 (m-80) REVERT: A 3138 TYR cc_start: 0.9322 (t80) cc_final: 0.8918 (t80) REVERT: A 3152 ARG cc_start: 0.8737 (ptp-170) cc_final: 0.8416 (ptp-170) REVERT: A 3159 LEU cc_start: 0.8870 (pp) cc_final: 0.7491 (pp) REVERT: A 3241 MET cc_start: 0.9220 (mmp) cc_final: 0.8474 (mmt) REVERT: A 3248 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8197 (ttt180) REVERT: A 3302 PHE cc_start: 0.8960 (m-80) cc_final: 0.8680 (m-80) REVERT: A 3304 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8543 (tp-100) REVERT: A 4035 TYR cc_start: 0.8206 (m-80) cc_final: 0.7822 (t80) REVERT: A 4046 ARG cc_start: 0.8516 (tpm170) cc_final: 0.8152 (tpp-160) REVERT: A 4274 MET cc_start: 0.4818 (ttm) cc_final: 0.3939 (mtp) REVERT: A 4707 MET cc_start: 0.8588 (ttp) cc_final: 0.8330 (ttt) REVERT: A 4804 MET cc_start: 0.9004 (mmp) cc_final: 0.8718 (mmm) REVERT: E 4 GLU cc_start: 0.7679 (mp0) cc_final: 0.7446 (mp0) REVERT: E 18 LYS cc_start: 0.9155 (mppt) cc_final: 0.8903 (mppt) REVERT: F 18 LYS cc_start: 0.9052 (mppt) cc_final: 0.8675 (mppt) REVERT: F 58 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8037 (ttpp) REVERT: F 62 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: G 4 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7437 (mp0) REVERT: G 18 LYS cc_start: 0.9159 (mppt) cc_final: 0.8721 (mppt) REVERT: H 81 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9229 (p) REVERT: B 81 MET cc_start: 0.8287 (tmm) cc_final: 0.7806 (tmm) REVERT: B 655 MET cc_start: 0.8676 (mmm) cc_final: 0.8108 (mmm) REVERT: B 890 HIS cc_start: 0.9313 (OUTLIER) cc_final: 0.8877 (p-80) REVERT: B 895 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9045 (pmm) REVERT: B 940 LEU cc_start: 0.9487 (mt) cc_final: 0.9246 (pp) REVERT: B 995 MET cc_start: 0.8830 (ttp) cc_final: 0.8298 (ttm) REVERT: B 999 LEU cc_start: 0.9157 (tt) cc_final: 0.8723 (mt) REVERT: B 2485 LEU cc_start: 0.9419 (mm) cc_final: 0.9195 (mm) REVERT: B 2585 MET cc_start: 0.7832 (ppp) cc_final: 0.7563 (ppp) REVERT: B 2666 LEU cc_start: 0.9489 (pp) cc_final: 0.9250 (pt) REVERT: B 2689 MET cc_start: 0.6389 (mtt) cc_final: 0.5860 (mtp) REVERT: B 2734 MET cc_start: 0.9053 (mmp) cc_final: 0.8808 (mmp) REVERT: B 2779 LEU cc_start: 0.9423 (mp) cc_final: 0.9044 (pt) REVERT: B 2844 MET cc_start: 0.8914 (ppp) cc_final: 0.8530 (ppp) REVERT: B 2893 LEU cc_start: 0.9563 (mp) cc_final: 0.9296 (mt) REVERT: B 2897 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 2921 PHE cc_start: 0.8686 (t80) cc_final: 0.8223 (t80) REVERT: B 2932 TYR cc_start: 0.8231 (t80) cc_final: 0.7913 (t80) REVERT: B 2938 GLN cc_start: 0.8944 (pp30) cc_final: 0.8500 (pp30) REVERT: B 2975 PHE cc_start: 0.8920 (m-80) cc_final: 0.8680 (m-80) REVERT: B 2982 PHE cc_start: 0.8762 (m-80) cc_final: 0.8137 (m-80) REVERT: B 3003 MET cc_start: 0.8621 (ptm) cc_final: 0.8253 (ptm) REVERT: B 3022 PHE cc_start: 0.7969 (m-80) cc_final: 0.7666 (m-80) REVERT: B 3031 ASN cc_start: 0.9211 (t0) cc_final: 0.8810 (t0) REVERT: B 3040 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 3068 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8912 (pt) REVERT: B 3069 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: B 3105 LEU cc_start: 0.9057 (mt) cc_final: 0.8656 (tt) REVERT: B 3138 TYR cc_start: 0.9325 (t80) cc_final: 0.8952 (t80) REVERT: B 3152 ARG cc_start: 0.8767 (ptp-170) cc_final: 0.8411 (ptp-170) REVERT: B 3159 LEU cc_start: 0.8873 (pp) cc_final: 0.7546 (pp) REVERT: B 3241 MET cc_start: 0.9205 (mmp) cc_final: 0.8434 (mmt) REVERT: B 3246 MET cc_start: 0.9051 (mtp) cc_final: 0.8801 (mtm) REVERT: B 3302 PHE cc_start: 0.8950 (m-80) cc_final: 0.8726 (m-80) REVERT: B 3304 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8625 (tp-100) REVERT: B 4035 TYR cc_start: 0.8209 (m-80) cc_final: 0.7793 (t80) REVERT: B 4046 ARG cc_start: 0.8542 (tpm170) cc_final: 0.8179 (tpp-160) REVERT: B 4274 MET cc_start: 0.4824 (ttm) cc_final: 0.3817 (mtp) REVERT: B 4672 MET cc_start: 0.8749 (mtm) cc_final: 0.8359 (mtm) REVERT: B 4707 MET cc_start: 0.8586 (ttp) cc_final: 0.8328 (ttt) REVERT: B 4726 MET cc_start: 0.8354 (tpt) cc_final: 0.7631 (tpp) REVERT: C 81 MET cc_start: 0.8301 (tmm) cc_final: 0.7807 (tmm) REVERT: C 655 MET cc_start: 0.8684 (mmm) cc_final: 0.8137 (mmm) REVERT: C 890 HIS cc_start: 0.9302 (OUTLIER) cc_final: 0.8845 (p-80) REVERT: C 895 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9045 (pmm) REVERT: C 940 LEU cc_start: 0.9487 (mt) cc_final: 0.9265 (pp) REVERT: C 995 MET cc_start: 0.8832 (ttp) cc_final: 0.8580 (ttm) REVERT: C 2485 LEU cc_start: 0.9410 (mm) cc_final: 0.9178 (mm) REVERT: C 2689 MET cc_start: 0.6763 (mtt) cc_final: 0.6336 (mtp) REVERT: C 2734 MET cc_start: 0.9036 (mmp) cc_final: 0.8739 (mmp) REVERT: C 2779 LEU cc_start: 0.9485 (mp) cc_final: 0.9165 (pt) REVERT: C 2840 MET cc_start: 0.8912 (mmt) cc_final: 0.7778 (mmt) REVERT: C 2843 MET cc_start: 0.8929 (ptt) cc_final: 0.8604 (ppp) REVERT: C 2844 MET cc_start: 0.8968 (ppp) cc_final: 0.8532 (ppp) REVERT: C 2895 PHE cc_start: 0.8988 (t80) cc_final: 0.8572 (t80) REVERT: C 2897 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8764 (tm-30) REVERT: C 2921 PHE cc_start: 0.8682 (t80) cc_final: 0.8316 (t80) REVERT: C 2932 TYR cc_start: 0.8215 (t80) cc_final: 0.7900 (t80) REVERT: C 2938 GLN cc_start: 0.8963 (pp30) cc_final: 0.8527 (pp30) REVERT: C 2975 PHE cc_start: 0.8897 (m-80) cc_final: 0.8654 (m-80) REVERT: C 2982 PHE cc_start: 0.8803 (m-80) cc_final: 0.8209 (m-80) REVERT: C 3003 MET cc_start: 0.8675 (ptm) cc_final: 0.8321 (ptm) REVERT: C 3022 PHE cc_start: 0.7943 (m-80) cc_final: 0.7672 (m-80) REVERT: C 3031 ASN cc_start: 0.9196 (t0) cc_final: 0.8801 (t0) REVERT: C 3040 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7438 (mt) REVERT: C 3068 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8918 (pt) REVERT: C 3069 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8296 (mm-30) REVERT: C 3138 TYR cc_start: 0.9324 (t80) cc_final: 0.8969 (t80) REVERT: C 3152 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8483 (ptp-170) REVERT: C 3159 LEU cc_start: 0.8899 (pp) cc_final: 0.7775 (pp) REVERT: C 3241 MET cc_start: 0.9203 (mmp) cc_final: 0.8399 (mmt) REVERT: C 3249 TRP cc_start: 0.8869 (m100) cc_final: 0.8459 (m100) REVERT: C 3302 PHE cc_start: 0.8945 (m-80) cc_final: 0.8686 (m-80) REVERT: C 3304 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8580 (tp-100) REVERT: C 4035 TYR cc_start: 0.8229 (m-80) cc_final: 0.7811 (t80) REVERT: C 4046 ARG cc_start: 0.8564 (tpm170) cc_final: 0.8173 (tpp-160) REVERT: C 4698 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8368 (mt) REVERT: C 4707 MET cc_start: 0.8600 (ttp) cc_final: 0.8346 (ttt) REVERT: D 81 MET cc_start: 0.8293 (tmm) cc_final: 0.7797 (tmm) REVERT: D 655 MET cc_start: 0.8651 (mmm) cc_final: 0.8181 (mmm) REVERT: D 890 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.8840 (p-80) REVERT: D 895 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9042 (pmm) REVERT: D 940 LEU cc_start: 0.9482 (mt) cc_final: 0.9251 (pp) REVERT: D 995 MET cc_start: 0.8838 (ttp) cc_final: 0.8580 (ttm) REVERT: D 2485 LEU cc_start: 0.9429 (mm) cc_final: 0.9206 (mm) REVERT: D 2666 LEU cc_start: 0.9498 (pp) cc_final: 0.9257 (pt) REVERT: D 2689 MET cc_start: 0.6669 (mtt) cc_final: 0.6259 (mtp) REVERT: D 2734 MET cc_start: 0.9049 (mmp) cc_final: 0.8764 (mmp) REVERT: D 2779 LEU cc_start: 0.9495 (mp) cc_final: 0.9158 (pt) REVERT: D 2844 MET cc_start: 0.8897 (ppp) cc_final: 0.8646 (ppp) REVERT: D 2890 GLN cc_start: 0.8885 (mp10) cc_final: 0.8508 (mp10) REVERT: D 2893 LEU cc_start: 0.9558 (mt) cc_final: 0.9318 (mt) REVERT: D 2895 PHE cc_start: 0.8983 (t80) cc_final: 0.8658 (t80) REVERT: D 2897 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8785 (tm-30) REVERT: D 2921 PHE cc_start: 0.8675 (t80) cc_final: 0.8221 (t80) REVERT: D 2932 TYR cc_start: 0.8229 (t80) cc_final: 0.7918 (t80) REVERT: D 2938 GLN cc_start: 0.8950 (pp30) cc_final: 0.8532 (pp30) REVERT: D 2975 PHE cc_start: 0.8931 (m-80) cc_final: 0.8685 (m-80) REVERT: D 2982 PHE cc_start: 0.8777 (m-80) cc_final: 0.8140 (m-80) REVERT: D 3003 MET cc_start: 0.8617 (ptm) cc_final: 0.8255 (ptm) REVERT: D 3031 ASN cc_start: 0.9209 (t0) cc_final: 0.8813 (t0) REVERT: D 3040 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7469 (mt) REVERT: D 3068 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8909 (pt) REVERT: D 3069 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: D 3138 TYR cc_start: 0.9334 (t80) cc_final: 0.8971 (t80) REVERT: D 3152 ARG cc_start: 0.8777 (ptp-170) cc_final: 0.8501 (ptp-170) REVERT: D 3159 LEU cc_start: 0.8897 (pp) cc_final: 0.7324 (pp) REVERT: D 3241 MET cc_start: 0.9207 (mmp) cc_final: 0.8400 (mmt) REVERT: D 3249 TRP cc_start: 0.8847 (m100) cc_final: 0.8431 (m100) REVERT: D 3302 PHE cc_start: 0.8950 (m-80) cc_final: 0.8705 (m-80) REVERT: D 3304 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8599 (tp-100) REVERT: D 4035 TYR cc_start: 0.8238 (m-80) cc_final: 0.7813 (t80) REVERT: D 4046 ARG cc_start: 0.8575 (tpm170) cc_final: 0.8081 (tpp-160) REVERT: D 4672 MET cc_start: 0.8606 (mtm) cc_final: 0.8159 (mtm) REVERT: D 4698 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8368 (mt) REVERT: D 4707 MET cc_start: 0.8602 (ttp) cc_final: 0.8248 (ttp) REVERT: D 4804 MET cc_start: 0.9039 (mmp) cc_final: 0.8702 (mmm) outliers start: 115 outliers final: 59 residues processed: 1144 average time/residue: 1.2470 time to fit residues: 2534.0851 Evaluate side-chains 1156 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1071 time to evaluate : 11.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 2172 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1628 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2980 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 952 optimal weight: 6.9990 chunk 1220 optimal weight: 1.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 40.0000 chunk 933 optimal weight: 5.9990 chunk 1665 optimal weight: 4.9990 chunk 1042 optimal weight: 8.9990 chunk 1015 optimal weight: 5.9990 chunk 768 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2541 HIS ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3905 ASN A3955 GLN A3975 GLN ** A4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN C3955 GLN C3975 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4558 HIS ** D4933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 141728 Z= 0.330 Angle : 0.656 18.712 191492 Z= 0.321 Chirality : 0.042 0.282 20988 Planarity : 0.004 0.131 24600 Dihedral : 5.330 69.523 19108 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 0.70 % Allowed : 8.20 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.06), residues: 17212 helix: 1.71 (0.06), residues: 8864 sheet: 0.10 (0.13), residues: 1588 loop : -0.36 (0.08), residues: 6760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B3249 HIS 0.023 0.001 HIS C3034 PHE 0.028 0.001 PHE B2895 TYR 0.027 0.001 TYR B3245 ARG 0.011 0.000 ARG H 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 1195 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1089 time to evaluate : 11.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8323 (tmm) cc_final: 0.7862 (tmm) REVERT: A 535 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: A 655 MET cc_start: 0.8685 (mmm) cc_final: 0.8071 (mmm) REVERT: A 890 HIS cc_start: 0.9328 (OUTLIER) cc_final: 0.8879 (p-80) REVERT: A 895 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9058 (pmm) REVERT: A 995 MET cc_start: 0.8822 (ttp) cc_final: 0.8565 (ttm) REVERT: A 2485 LEU cc_start: 0.9433 (mm) cc_final: 0.9207 (mm) REVERT: A 2610 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9091 (mm) REVERT: A 2734 MET cc_start: 0.9131 (mmp) cc_final: 0.8842 (mmp) REVERT: A 2779 LEU cc_start: 0.9435 (mp) cc_final: 0.9051 (pt) REVERT: A 2840 MET cc_start: 0.9240 (mmt) cc_final: 0.8955 (mmt) REVERT: A 2844 MET cc_start: 0.8945 (ppp) cc_final: 0.8660 (ppp) REVERT: A 2848 TYR cc_start: 0.8974 (m-10) cc_final: 0.8744 (m-80) REVERT: A 2893 LEU cc_start: 0.9610 (mt) cc_final: 0.9292 (pp) REVERT: A 2897 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 2921 PHE cc_start: 0.8646 (t80) cc_final: 0.8126 (t80) REVERT: A 2932 TYR cc_start: 0.8327 (t80) cc_final: 0.7999 (t80) REVERT: A 2938 GLN cc_start: 0.8936 (pp30) cc_final: 0.8488 (pp30) REVERT: A 2975 PHE cc_start: 0.8982 (m-80) cc_final: 0.8731 (m-80) REVERT: A 2982 PHE cc_start: 0.8801 (m-80) cc_final: 0.8198 (m-80) REVERT: A 3003 MET cc_start: 0.8600 (ptm) cc_final: 0.8210 (ptm) REVERT: A 3022 PHE cc_start: 0.8041 (m-80) cc_final: 0.7724 (m-80) REVERT: A 3031 ASN cc_start: 0.9208 (t0) cc_final: 0.8820 (t0) REVERT: A 3040 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7225 (mt) REVERT: A 3068 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8926 (pt) REVERT: A 3069 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: A 3105 LEU cc_start: 0.9052 (mm) cc_final: 0.8501 (tt) REVERT: A 3109 PHE cc_start: 0.9342 (m-10) cc_final: 0.8961 (m-80) REVERT: A 3138 TYR cc_start: 0.9329 (t80) cc_final: 0.8949 (t80) REVERT: A 3152 ARG cc_start: 0.8807 (ptp-170) cc_final: 0.8537 (ptp-170) REVERT: A 3159 LEU cc_start: 0.8881 (pp) cc_final: 0.7539 (pp) REVERT: A 3162 PHE cc_start: 0.9008 (t80) cc_final: 0.8786 (t80) REVERT: A 3166 PHE cc_start: 0.8923 (t80) cc_final: 0.7752 (t80) REVERT: A 3231 MET cc_start: 0.8180 (tmm) cc_final: 0.7950 (tmm) REVERT: A 3241 MET cc_start: 0.9237 (mmp) cc_final: 0.8552 (mmt) REVERT: A 3248 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8238 (ttt180) REVERT: A 3302 PHE cc_start: 0.8973 (m-80) cc_final: 0.8749 (m-80) REVERT: A 3304 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8576 (tp-100) REVERT: A 4035 TYR cc_start: 0.8215 (m-80) cc_final: 0.7828 (t80) REVERT: A 4274 MET cc_start: 0.4916 (ttm) cc_final: 0.3998 (mtp) REVERT: A 4672 MET cc_start: 0.8597 (mtm) cc_final: 0.8232 (mtm) REVERT: A 4707 MET cc_start: 0.8589 (ttp) cc_final: 0.8330 (ttt) REVERT: A 4804 MET cc_start: 0.9030 (mmp) cc_final: 0.8732 (mmm) REVERT: E 4 GLU cc_start: 0.7675 (mp0) cc_final: 0.7444 (mp0) REVERT: E 18 LYS cc_start: 0.9168 (mppt) cc_final: 0.8895 (mppt) REVERT: F 18 LYS cc_start: 0.9082 (mppt) cc_final: 0.8738 (mppt) REVERT: F 58 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8078 (ttpp) REVERT: F 62 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: F 67 MET cc_start: 0.8830 (mtp) cc_final: 0.8612 (mtp) REVERT: G 4 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7441 (mp0) REVERT: G 18 LYS cc_start: 0.9167 (mppt) cc_final: 0.8716 (mppt) REVERT: H 81 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9195 (p) REVERT: B 81 MET cc_start: 0.8296 (tmm) cc_final: 0.7809 (tmm) REVERT: B 655 MET cc_start: 0.8711 (mmm) cc_final: 0.8113 (mmm) REVERT: B 661 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9074 (pp) REVERT: B 890 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.8876 (p-80) REVERT: B 895 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9083 (pmm) REVERT: B 940 LEU cc_start: 0.9493 (mt) cc_final: 0.9259 (pp) REVERT: B 995 MET cc_start: 0.8851 (ttp) cc_final: 0.8319 (ttm) REVERT: B 999 LEU cc_start: 0.9185 (tt) cc_final: 0.8751 (mt) REVERT: B 2485 LEU cc_start: 0.9434 (mm) cc_final: 0.9206 (mm) REVERT: B 2585 MET cc_start: 0.7896 (ppp) cc_final: 0.7619 (ppp) REVERT: B 2734 MET cc_start: 0.9107 (mmp) cc_final: 0.8798 (mmp) REVERT: B 2837 LEU cc_start: 0.9526 (mt) cc_final: 0.9288 (mt) REVERT: B 2840 MET cc_start: 0.8951 (tpp) cc_final: 0.8556 (mmm) REVERT: B 2843 MET cc_start: 0.9076 (ptt) cc_final: 0.8666 (ppp) REVERT: B 2844 MET cc_start: 0.8886 (ppp) cc_final: 0.8538 (ppp) REVERT: B 2893 LEU cc_start: 0.9571 (mp) cc_final: 0.9272 (mt) REVERT: B 2895 PHE cc_start: 0.8866 (t80) cc_final: 0.8572 (t80) REVERT: B 2897 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 2921 PHE cc_start: 0.8672 (t80) cc_final: 0.8162 (t80) REVERT: B 2932 TYR cc_start: 0.8270 (t80) cc_final: 0.7945 (t80) REVERT: B 2938 GLN cc_start: 0.8957 (pp30) cc_final: 0.8493 (pp30) REVERT: B 2975 PHE cc_start: 0.8969 (m-80) cc_final: 0.8703 (m-80) REVERT: B 2982 PHE cc_start: 0.8802 (m-80) cc_final: 0.8174 (m-80) REVERT: B 3003 MET cc_start: 0.8635 (ptm) cc_final: 0.8236 (ptm) REVERT: B 3022 PHE cc_start: 0.7993 (m-80) cc_final: 0.7703 (m-80) REVERT: B 3031 ASN cc_start: 0.9222 (t0) cc_final: 0.8824 (t0) REVERT: B 3040 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7465 (mt) REVERT: B 3068 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8883 (pt) REVERT: B 3069 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: B 3105 LEU cc_start: 0.9085 (mt) cc_final: 0.8534 (tt) REVERT: B 3109 PHE cc_start: 0.9281 (m-80) cc_final: 0.8829 (m-80) REVERT: B 3138 TYR cc_start: 0.9325 (t80) cc_final: 0.8978 (t80) REVERT: B 3152 ARG cc_start: 0.8829 (ptp-170) cc_final: 0.8532 (ptp-170) REVERT: B 3159 LEU cc_start: 0.8870 (pp) cc_final: 0.7576 (pp) REVERT: B 3231 MET cc_start: 0.8136 (tmm) cc_final: 0.7898 (tmm) REVERT: B 3241 MET cc_start: 0.9235 (mmp) cc_final: 0.8480 (mmt) REVERT: B 3246 MET cc_start: 0.9056 (mtp) cc_final: 0.8814 (mtm) REVERT: B 3302 PHE cc_start: 0.8962 (m-80) cc_final: 0.8741 (m-80) REVERT: B 3304 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8620 (tp-100) REVERT: B 4035 TYR cc_start: 0.8224 (m-80) cc_final: 0.7814 (t80) REVERT: B 4707 MET cc_start: 0.8603 (ttp) cc_final: 0.8339 (ttt) REVERT: B 4726 MET cc_start: 0.8361 (tpt) cc_final: 0.7613 (tpp) REVERT: C 81 MET cc_start: 0.8310 (tmm) cc_final: 0.7819 (tmm) REVERT: C 890 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8852 (p-80) REVERT: C 895 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9099 (pmm) REVERT: C 940 LEU cc_start: 0.9493 (mt) cc_final: 0.9282 (pp) REVERT: C 995 MET cc_start: 0.8859 (ttp) cc_final: 0.8613 (ttm) REVERT: C 2485 LEU cc_start: 0.9427 (mm) cc_final: 0.9205 (mm) REVERT: C 2689 MET cc_start: 0.6744 (mtt) cc_final: 0.6337 (mtp) REVERT: C 2734 MET cc_start: 0.9102 (mmp) cc_final: 0.8792 (mmp) REVERT: C 2840 MET cc_start: 0.9244 (mmt) cc_final: 0.8272 (mmt) REVERT: C 2843 MET cc_start: 0.8963 (ptt) cc_final: 0.8667 (ppp) REVERT: C 2844 MET cc_start: 0.8982 (ppp) cc_final: 0.8610 (ppp) REVERT: C 2893 LEU cc_start: 0.9581 (mt) cc_final: 0.9366 (tt) REVERT: C 2895 PHE cc_start: 0.9016 (t80) cc_final: 0.8625 (t80) REVERT: C 2897 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8816 (tm-30) REVERT: C 2921 PHE cc_start: 0.8696 (t80) cc_final: 0.8297 (t80) REVERT: C 2932 TYR cc_start: 0.8232 (t80) cc_final: 0.7910 (t80) REVERT: C 2938 GLN cc_start: 0.8974 (pp30) cc_final: 0.8514 (pp30) REVERT: C 2975 PHE cc_start: 0.8910 (m-80) cc_final: 0.8653 (m-80) REVERT: C 2982 PHE cc_start: 0.8822 (m-80) cc_final: 0.8219 (m-80) REVERT: C 3003 MET cc_start: 0.8689 (ptm) cc_final: 0.8298 (ptm) REVERT: C 3022 PHE cc_start: 0.7989 (m-80) cc_final: 0.7701 (m-80) REVERT: C 3031 ASN cc_start: 0.9194 (t0) cc_final: 0.8802 (t0) REVERT: C 3040 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7444 (mt) REVERT: C 3068 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8908 (pt) REVERT: C 3069 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: C 3138 TYR cc_start: 0.9325 (t80) cc_final: 0.8990 (t80) REVERT: C 3152 ARG cc_start: 0.8801 (ptp-170) cc_final: 0.8508 (ptp-170) REVERT: C 3159 LEU cc_start: 0.8878 (pp) cc_final: 0.7674 (pp) REVERT: C 3231 MET cc_start: 0.8131 (tmm) cc_final: 0.7876 (tmm) REVERT: C 3241 MET cc_start: 0.9217 (mmp) cc_final: 0.8445 (mmt) REVERT: C 3249 TRP cc_start: 0.8818 (m100) cc_final: 0.8418 (m100) REVERT: C 3302 PHE cc_start: 0.8969 (m-80) cc_final: 0.8709 (m-80) REVERT: C 3304 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8555 (tp-100) REVERT: C 4035 TYR cc_start: 0.8226 (m-80) cc_final: 0.7812 (t80) REVERT: C 4672 MET cc_start: 0.8598 (mtm) cc_final: 0.8242 (mtm) REVERT: C 4698 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8366 (mt) REVERT: C 4707 MET cc_start: 0.8600 (ttp) cc_final: 0.8259 (ttp) REVERT: D 81 MET cc_start: 0.8298 (tmm) cc_final: 0.7805 (tmm) REVERT: D 535 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: D 655 MET cc_start: 0.8704 (mmm) cc_final: 0.8216 (mmm) REVERT: D 890 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.8845 (p-80) REVERT: D 895 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9074 (pmm) REVERT: D 940 LEU cc_start: 0.9489 (mt) cc_final: 0.9264 (pp) REVERT: D 995 MET cc_start: 0.8862 (ttp) cc_final: 0.8608 (ttm) REVERT: D 2485 LEU cc_start: 0.9437 (mm) cc_final: 0.9213 (mm) REVERT: D 2689 MET cc_start: 0.6635 (mtt) cc_final: 0.6220 (mtp) REVERT: D 2734 MET cc_start: 0.9000 (mmp) cc_final: 0.8760 (mmp) REVERT: D 2779 LEU cc_start: 0.9519 (mp) cc_final: 0.9172 (pt) REVERT: D 2833 LEU cc_start: 0.8960 (mt) cc_final: 0.8759 (mt) REVERT: D 2844 MET cc_start: 0.8919 (ppp) cc_final: 0.8640 (ppp) REVERT: D 2890 GLN cc_start: 0.8904 (mp10) cc_final: 0.8478 (mp10) REVERT: D 2895 PHE cc_start: 0.9015 (t80) cc_final: 0.8695 (t80) REVERT: D 2897 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8812 (tm-30) REVERT: D 2921 PHE cc_start: 0.8671 (t80) cc_final: 0.8165 (t80) REVERT: D 2932 TYR cc_start: 0.8242 (t80) cc_final: 0.7928 (t80) REVERT: D 2938 GLN cc_start: 0.8963 (pp30) cc_final: 0.8520 (pp30) REVERT: D 2975 PHE cc_start: 0.8938 (m-80) cc_final: 0.8677 (m-80) REVERT: D 2982 PHE cc_start: 0.8797 (m-80) cc_final: 0.8171 (m-80) REVERT: D 3003 MET cc_start: 0.8625 (ptm) cc_final: 0.8229 (ptm) REVERT: D 3031 ASN cc_start: 0.9219 (t0) cc_final: 0.8819 (t0) REVERT: D 3040 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7447 (mt) REVERT: D 3068 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8890 (pt) REVERT: D 3069 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: D 3105 LEU cc_start: 0.9057 (mt) cc_final: 0.8577 (tt) REVERT: D 3138 TYR cc_start: 0.9341 (t80) cc_final: 0.9009 (t80) REVERT: D 3152 ARG cc_start: 0.8818 (ptp-170) cc_final: 0.8524 (ptp-170) REVERT: D 3159 LEU cc_start: 0.8886 (pp) cc_final: 0.7253 (pp) REVERT: D 3231 MET cc_start: 0.8130 (tmm) cc_final: 0.7885 (tmm) REVERT: D 3241 MET cc_start: 0.9222 (mmp) cc_final: 0.8458 (mmt) REVERT: D 3249 TRP cc_start: 0.8865 (m100) cc_final: 0.8457 (m100) REVERT: D 3302 PHE cc_start: 0.8979 (m-80) cc_final: 0.8740 (m-80) REVERT: D 3304 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8629 (tp-100) REVERT: D 4035 TYR cc_start: 0.8241 (m-80) cc_final: 0.7822 (t80) REVERT: D 4672 MET cc_start: 0.8613 (mtm) cc_final: 0.8117 (mtm) REVERT: D 4698 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 4707 MET cc_start: 0.8618 (ttp) cc_final: 0.8277 (ttp) outliers start: 106 outliers final: 58 residues processed: 1132 average time/residue: 1.2053 time to fit residues: 2414.8581 Evaluate side-chains 1161 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1075 time to evaluate : 11.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 2172 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3296 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 2172 MET Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3296 MET Chi-restraints excluded: chain C residue 3686 PHE Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1628 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2980 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3262 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3296 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 9.9990 chunk 665 optimal weight: 5.9990 chunk 994 optimal weight: 4.9990 chunk 501 optimal weight: 20.0000 chunk 327 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 1058 optimal weight: 6.9990 chunk 1134 optimal weight: 30.0000 chunk 823 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 1309 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2838 HIS A A2838 HIS B ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN A4558 HIS ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN C3955 GLN C3975 GLN C4558 HIS C4961 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN D3955 GLN D3975 GLN D4558 HIS D4961 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 141728 Z= 0.243 Angle : 0.654 19.384 191492 Z= 0.316 Chirality : 0.041 0.328 20988 Planarity : 0.004 0.129 24600 Dihedral : 5.211 69.505 19108 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 0.71 % Allowed : 8.46 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.07), residues: 17212 helix: 1.73 (0.06), residues: 8868 sheet: 0.08 (0.13), residues: 1620 loop : -0.34 (0.08), residues: 6724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B3249 HIS 0.023 0.001 HIS C3034 PHE 0.046 0.001 PHE B3162 TYR 0.035 0.001 TYR B3245 ARG 0.021 0.000 ARG B1051 *********************** 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 1184 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1076 time to evaluate : 11.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8318 (tmm) cc_final: 0.7847 (tmm) REVERT: A 535 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 655 MET cc_start: 0.8657 (mmm) cc_final: 0.8166 (mmm) REVERT: A 890 HIS cc_start: 0.9330 (OUTLIER) cc_final: 0.8868 (p-80) REVERT: A 895 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9070 (pmm) REVERT: A 995 MET cc_start: 0.8827 (ttp) cc_final: 0.8567 (ttm) REVERT: A 2485 LEU cc_start: 0.9423 (mm) cc_final: 0.9195 (mm) REVERT: A 2610 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 2734 MET cc_start: 0.9000 (mmp) cc_final: 0.8628 (mmp) REVERT: A 2779 LEU cc_start: 0.9448 (mp) cc_final: 0.9089 (pt) REVERT: A 2840 MET cc_start: 0.9222 (mmt) cc_final: 0.8889 (mmt) REVERT: A 2893 LEU cc_start: 0.9589 (mt) cc_final: 0.9314 (tt) REVERT: A 2895 PHE cc_start: 0.8864 (t80) cc_final: 0.8557 (t80) REVERT: A 2921 PHE cc_start: 0.8581 (t80) cc_final: 0.8046 (t80) REVERT: A 2932 TYR cc_start: 0.8303 (t80) cc_final: 0.7983 (t80) REVERT: A 2975 PHE cc_start: 0.8965 (m-80) cc_final: 0.8704 (m-80) REVERT: A 2982 PHE cc_start: 0.8772 (m-80) cc_final: 0.8169 (m-80) REVERT: A 3003 MET cc_start: 0.8591 (ptm) cc_final: 0.8240 (ptm) REVERT: A 3022 PHE cc_start: 0.8049 (m-80) cc_final: 0.7748 (m-80) REVERT: A 3031 ASN cc_start: 0.9197 (t0) cc_final: 0.8776 (t0) REVERT: A 3040 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7224 (mt) REVERT: A 3068 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8900 (pt) REVERT: A 3069 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: A 3105 LEU cc_start: 0.9043 (mm) cc_final: 0.8497 (tt) REVERT: A 3109 PHE cc_start: 0.9322 (m-10) cc_final: 0.8923 (m-80) REVERT: A 3138 TYR cc_start: 0.9307 (t80) cc_final: 0.8915 (t80) REVERT: A 3152 ARG cc_start: 0.8828 (ptp-170) cc_final: 0.8524 (ptp-170) REVERT: A 3159 LEU cc_start: 0.8882 (pp) cc_final: 0.7129 (pp) REVERT: A 3162 PHE cc_start: 0.8968 (t80) cc_final: 0.8719 (t80) REVERT: A 3231 MET cc_start: 0.8097 (tmm) cc_final: 0.7867 (tmm) REVERT: A 3241 MET cc_start: 0.9245 (mmp) cc_final: 0.8498 (mmt) REVERT: A 3249 TRP cc_start: 0.8686 (m100) cc_final: 0.8411 (m100) REVERT: A 3304 GLN cc_start: 0.8887 (tp-100) cc_final: 0.8536 (tp-100) REVERT: A 3819 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6706 (ptt) REVERT: A 4035 TYR cc_start: 0.8219 (m-80) cc_final: 0.7846 (t80) REVERT: A 4274 MET cc_start: 0.4872 (ttm) cc_final: 0.4134 (mtp) REVERT: A 4672 MET cc_start: 0.8606 (mtm) cc_final: 0.8338 (mtm) REVERT: A 4707 MET cc_start: 0.8582 (ttp) cc_final: 0.8325 (ttt) REVERT: A 4804 MET cc_start: 0.9014 (mmp) cc_final: 0.8715 (mmm) REVERT: E 18 LYS cc_start: 0.9173 (mppt) cc_final: 0.8898 (mppt) REVERT: F 18 LYS cc_start: 0.9103 (mppt) cc_final: 0.8786 (mppt) REVERT: F 58 LYS cc_start: 0.8807 (ttpp) cc_final: 0.7997 (ttpp) REVERT: F 62 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: F 67 MET cc_start: 0.8733 (mtp) cc_final: 0.8455 (mtp) REVERT: G 4 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7425 (mp0) REVERT: G 18 LYS cc_start: 0.9162 (mppt) cc_final: 0.8717 (mppt) REVERT: H 81 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9265 (p) REVERT: B 81 MET cc_start: 0.8296 (tmm) cc_final: 0.7807 (tmm) REVERT: B 661 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9068 (pp) REVERT: B 890 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8870 (p-80) REVERT: B 940 LEU cc_start: 0.9491 (mt) cc_final: 0.9243 (pp) REVERT: B 995 MET cc_start: 0.8834 (ttp) cc_final: 0.8284 (ttm) REVERT: B 999 LEU cc_start: 0.9159 (tt) cc_final: 0.8707 (mt) REVERT: B 2485 LEU cc_start: 0.9426 (mm) cc_final: 0.9197 (mm) REVERT: B 2585 MET cc_start: 0.7845 (ppp) cc_final: 0.7557 (ppp) REVERT: B 2734 MET cc_start: 0.9100 (mmp) cc_final: 0.8818 (mmp) REVERT: B 2779 LEU cc_start: 0.9442 (mp) cc_final: 0.9096 (pt) REVERT: B 2844 MET cc_start: 0.8927 (ppp) cc_final: 0.8582 (ppp) REVERT: B 2893 LEU cc_start: 0.9550 (mp) cc_final: 0.9263 (mm) REVERT: B 2895 PHE cc_start: 0.8861 (t80) cc_final: 0.8424 (t80) REVERT: B 2897 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8695 (tm-30) REVERT: B 2921 PHE cc_start: 0.8619 (t80) cc_final: 0.8079 (t80) REVERT: B 2932 TYR cc_start: 0.8237 (t80) cc_final: 0.7919 (t80) REVERT: B 2938 GLN cc_start: 0.8953 (pp30) cc_final: 0.8474 (pp30) REVERT: B 2975 PHE cc_start: 0.8928 (m-80) cc_final: 0.8653 (m-80) REVERT: B 2982 PHE cc_start: 0.8787 (m-80) cc_final: 0.8159 (m-80) REVERT: B 3003 MET cc_start: 0.8617 (ptm) cc_final: 0.8231 (ptm) REVERT: B 3022 PHE cc_start: 0.8000 (m-80) cc_final: 0.7689 (m-80) REVERT: B 3031 ASN cc_start: 0.9211 (t0) cc_final: 0.8753 (t0) REVERT: B 3040 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7445 (mt) REVERT: B 3068 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8884 (pt) REVERT: B 3069 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8368 (mm-30) REVERT: B 3105 LEU cc_start: 0.9084 (mt) cc_final: 0.8560 (tt) REVERT: B 3109 PHE cc_start: 0.9286 (m-80) cc_final: 0.8833 (m-80) REVERT: B 3138 TYR cc_start: 0.9319 (t80) cc_final: 0.8961 (t80) REVERT: B 3152 ARG cc_start: 0.8828 (ptp-170) cc_final: 0.8240 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8883 (pp) cc_final: 0.7140 (pp) REVERT: B 3231 MET cc_start: 0.8078 (tmm) cc_final: 0.7827 (tmm) REVERT: B 3241 MET cc_start: 0.9217 (mmp) cc_final: 0.8463 (mmt) REVERT: B 3302 PHE cc_start: 0.8944 (m-80) cc_final: 0.8743 (m-80) REVERT: B 3304 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8599 (tp-100) REVERT: B 3739 MET cc_start: 0.9038 (ttp) cc_final: 0.8731 (ttp) REVERT: B 4035 TYR cc_start: 0.8235 (m-80) cc_final: 0.7846 (t80) REVERT: B 4672 MET cc_start: 0.8645 (mtm) cc_final: 0.8274 (mtm) REVERT: B 4707 MET cc_start: 0.8586 (ttp) cc_final: 0.8320 (ttt) REVERT: C 81 MET cc_start: 0.8309 (tmm) cc_final: 0.7814 (tmm) REVERT: C 890 HIS cc_start: 0.9300 (OUTLIER) cc_final: 0.8841 (p-80) REVERT: C 895 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9098 (pmm) REVERT: C 940 LEU cc_start: 0.9487 (mt) cc_final: 0.9272 (pp) REVERT: C 995 MET cc_start: 0.8841 (ttp) cc_final: 0.8592 (ttm) REVERT: C 2485 LEU cc_start: 0.9416 (mm) cc_final: 0.9193 (mm) REVERT: C 2734 MET cc_start: 0.9091 (mmp) cc_final: 0.8752 (mmp) REVERT: C 2779 LEU cc_start: 0.9505 (mp) cc_final: 0.9252 (pt) REVERT: C 2837 LEU cc_start: 0.9557 (mt) cc_final: 0.9275 (mp) REVERT: C 2840 MET cc_start: 0.9213 (mmt) cc_final: 0.9004 (mmt) REVERT: C 2844 MET cc_start: 0.8951 (ppp) cc_final: 0.8741 (ppp) REVERT: C 2893 LEU cc_start: 0.9578 (mt) cc_final: 0.9289 (pp) REVERT: C 2895 PHE cc_start: 0.8981 (t80) cc_final: 0.8664 (t80) REVERT: C 2897 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8807 (tm-30) REVERT: C 2932 TYR cc_start: 0.8217 (t80) cc_final: 0.7903 (t80) REVERT: C 2938 GLN cc_start: 0.8958 (pp30) cc_final: 0.8501 (pp30) REVERT: C 2975 PHE cc_start: 0.8896 (m-80) cc_final: 0.8628 (m-80) REVERT: C 2982 PHE cc_start: 0.8792 (m-80) cc_final: 0.8190 (m-80) REVERT: C 3003 MET cc_start: 0.8663 (ptm) cc_final: 0.8286 (ptm) REVERT: C 3022 PHE cc_start: 0.7942 (m-80) cc_final: 0.7676 (m-80) REVERT: C 3031 ASN cc_start: 0.9185 (t0) cc_final: 0.8806 (t0) REVERT: C 3040 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7430 (mt) REVERT: C 3068 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8882 (pt) REVERT: C 3069 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: C 3138 TYR cc_start: 0.9266 (t80) cc_final: 0.8964 (t80) REVERT: C 3152 ARG cc_start: 0.8792 (ptp-170) cc_final: 0.8237 (ptp-110) REVERT: C 3159 LEU cc_start: 0.8878 (pp) cc_final: 0.7620 (pp) REVERT: C 3231 MET cc_start: 0.8060 (tmm) cc_final: 0.7807 (tmm) REVERT: C 3241 MET cc_start: 0.9204 (mmp) cc_final: 0.8439 (mmt) REVERT: C 3249 TRP cc_start: 0.8782 (m100) cc_final: 0.8380 (m100) REVERT: C 3302 PHE cc_start: 0.8944 (m-80) cc_final: 0.8709 (m-80) REVERT: C 3304 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8546 (tp-100) REVERT: C 4035 TYR cc_start: 0.8209 (m-80) cc_final: 0.7852 (t80) REVERT: C 4672 MET cc_start: 0.8598 (mtm) cc_final: 0.8345 (mtm) REVERT: C 4698 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 4707 MET cc_start: 0.8588 (ttp) cc_final: 0.8245 (ttp) REVERT: C 4726 MET cc_start: 0.8413 (tpt) cc_final: 0.8190 (tpt) REVERT: D 81 MET cc_start: 0.8295 (tmm) cc_final: 0.7791 (tmm) REVERT: D 535 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: D 655 MET cc_start: 0.8657 (mmm) cc_final: 0.8205 (mmm) REVERT: D 890 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.8833 (p-80) REVERT: D 895 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9096 (pmm) REVERT: D 940 LEU cc_start: 0.9479 (mt) cc_final: 0.9260 (pp) REVERT: D 995 MET cc_start: 0.8852 (ttp) cc_final: 0.8596 (ttm) REVERT: D 2485 LEU cc_start: 0.9423 (mm) cc_final: 0.9199 (mm) REVERT: D 2734 MET cc_start: 0.9085 (mmp) cc_final: 0.8808 (mmp) REVERT: D 2779 LEU cc_start: 0.9505 (mp) cc_final: 0.9149 (pt) REVERT: D 2844 MET cc_start: 0.8887 (ppp) cc_final: 0.8647 (ppp) REVERT: D 2895 PHE cc_start: 0.9021 (t80) cc_final: 0.8718 (t80) REVERT: D 2897 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8839 (tm-30) REVERT: D 2921 PHE cc_start: 0.8622 (t80) cc_final: 0.8082 (t80) REVERT: D 2932 TYR cc_start: 0.8221 (t80) cc_final: 0.7906 (t80) REVERT: D 2938 GLN cc_start: 0.8943 (pp30) cc_final: 0.8497 (pp30) REVERT: D 2975 PHE cc_start: 0.8931 (m-80) cc_final: 0.8653 (m-80) REVERT: D 2982 PHE cc_start: 0.8765 (m-80) cc_final: 0.8139 (m-80) REVERT: D 3003 MET cc_start: 0.8623 (ptm) cc_final: 0.8249 (ptm) REVERT: D 3031 ASN cc_start: 0.9201 (t0) cc_final: 0.8803 (t0) REVERT: D 3040 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7442 (mt) REVERT: D 3068 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8880 (pt) REVERT: D 3069 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: D 3105 LEU cc_start: 0.9072 (mt) cc_final: 0.8642 (tt) REVERT: D 3138 TYR cc_start: 0.9326 (t80) cc_final: 0.9010 (t80) REVERT: D 3152 ARG cc_start: 0.8824 (ptp-170) cc_final: 0.8296 (ptp-110) REVERT: D 3159 LEU cc_start: 0.8873 (pp) cc_final: 0.7181 (pp) REVERT: D 3231 MET cc_start: 0.8106 (tmm) cc_final: 0.7866 (tmm) REVERT: D 3241 MET cc_start: 0.9227 (mmp) cc_final: 0.8451 (mmt) REVERT: D 3249 TRP cc_start: 0.8772 (m100) cc_final: 0.8358 (m100) REVERT: D 3302 PHE cc_start: 0.8967 (m-80) cc_final: 0.8743 (m-80) REVERT: D 3304 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8626 (tp-100) REVERT: D 4672 MET cc_start: 0.8601 (mtm) cc_final: 0.8095 (mtm) REVERT: D 4698 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8363 (mt) REVERT: D 4707 MET cc_start: 0.8591 (ttp) cc_final: 0.8255 (ttp) REVERT: D 4726 MET cc_start: 0.8426 (tpt) cc_final: 0.8203 (tpt) REVERT: D 4804 MET cc_start: 0.9020 (mmp) cc_final: 0.8715 (mmm) outliers start: 108 outliers final: 64 residues processed: 1118 average time/residue: 1.1826 time to fit residues: 2336.1101 Evaluate side-chains 1158 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1066 time to evaluate : 11.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 2172 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3819 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2172 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2760 TYR Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2760 TYR Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3273 MET Chi-restraints excluded: chain C residue 3686 PHE Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1628 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2760 TYR Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 3262 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 8.9990 chunk 1595 optimal weight: 0.6980 chunk 1455 optimal weight: 7.9990 chunk 1552 optimal weight: 4.9990 chunk 934 optimal weight: 8.9990 chunk 676 optimal weight: 10.0000 chunk 1218 optimal weight: 0.9980 chunk 476 optimal weight: 10.0000 chunk 1402 optimal weight: 10.0000 chunk 1467 optimal weight: 1.9990 chunk 1546 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 GLN ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN A4558 HIS F 21 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2838 HIS A B2838 HIS B B2928 GLN ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 GLN ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2838 HIS A C2838 HIS B ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN C3955 GLN C3975 GLN C4558 HIS ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4558 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 141728 Z= 0.267 Angle : 0.659 20.403 191492 Z= 0.319 Chirality : 0.042 0.301 20988 Planarity : 0.004 0.128 24600 Dihedral : 5.109 69.236 19108 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 0.65 % Allowed : 8.59 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.07), residues: 17212 helix: 1.73 (0.06), residues: 8872 sheet: 0.07 (0.13), residues: 1620 loop : -0.33 (0.08), residues: 6720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B3249 HIS 0.023 0.001 HIS A3034 PHE 0.035 0.001 PHE A2701 TYR 0.030 0.001 TYR B3245 ARG 0.016 0.000 ARG B1051 *********************** 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 1173 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1074 time to evaluate : 11.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8322 (tmm) cc_final: 0.7848 (tmm) REVERT: A 535 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 655 MET cc_start: 0.8664 (mmm) cc_final: 0.8161 (mmm) REVERT: A 890 HIS cc_start: 0.9330 (OUTLIER) cc_final: 0.8764 (p-80) REVERT: A 895 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8472 (ptt) REVERT: A 995 MET cc_start: 0.8834 (ttp) cc_final: 0.8573 (ttm) REVERT: A 2485 LEU cc_start: 0.9424 (mm) cc_final: 0.9194 (mm) REVERT: A 2610 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 2734 MET cc_start: 0.9001 (mmp) cc_final: 0.8643 (mmp) REVERT: A 2779 LEU cc_start: 0.9427 (mp) cc_final: 0.9060 (pt) REVERT: A 2840 MET cc_start: 0.9289 (mmt) cc_final: 0.8434 (mmt) REVERT: A 2843 MET cc_start: 0.8959 (ptp) cc_final: 0.8648 (pmm) REVERT: A 2890 GLN cc_start: 0.8921 (mp10) cc_final: 0.8493 (pm20) REVERT: A 2895 PHE cc_start: 0.8894 (t80) cc_final: 0.8330 (t80) REVERT: A 2921 PHE cc_start: 0.8571 (t80) cc_final: 0.8026 (t80) REVERT: A 2932 TYR cc_start: 0.8286 (t80) cc_final: 0.7973 (t80) REVERT: A 2938 GLN cc_start: 0.8939 (pp30) cc_final: 0.8484 (pp30) REVERT: A 2975 PHE cc_start: 0.8968 (m-80) cc_final: 0.8701 (m-80) REVERT: A 2982 PHE cc_start: 0.8773 (m-80) cc_final: 0.8163 (m-80) REVERT: A 3003 MET cc_start: 0.8587 (ptm) cc_final: 0.8238 (ptm) REVERT: A 3022 PHE cc_start: 0.8058 (m-80) cc_final: 0.7758 (m-80) REVERT: A 3031 ASN cc_start: 0.9192 (t0) cc_final: 0.8775 (t0) REVERT: A 3040 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 3068 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8875 (pt) REVERT: A 3069 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: A 3105 LEU cc_start: 0.9050 (mm) cc_final: 0.8490 (tt) REVERT: A 3109 PHE cc_start: 0.9331 (m-10) cc_final: 0.8914 (m-80) REVERT: A 3138 TYR cc_start: 0.9319 (t80) cc_final: 0.8938 (t80) REVERT: A 3152 ARG cc_start: 0.8848 (ptp-170) cc_final: 0.8289 (ptp-110) REVERT: A 3159 LEU cc_start: 0.8885 (pp) cc_final: 0.7079 (pp) REVERT: A 3162 PHE cc_start: 0.8980 (t80) cc_final: 0.8713 (t80) REVERT: A 3231 MET cc_start: 0.8127 (tmm) cc_final: 0.7895 (tmm) REVERT: A 3241 MET cc_start: 0.9236 (mmp) cc_final: 0.8461 (mmt) REVERT: A 3249 TRP cc_start: 0.8636 (m100) cc_final: 0.8391 (m100) REVERT: A 3304 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8534 (tp-100) REVERT: A 4274 MET cc_start: 0.4844 (ttm) cc_final: 0.4098 (mtp) REVERT: A 4672 MET cc_start: 0.8601 (mtm) cc_final: 0.8352 (mtm) REVERT: A 4707 MET cc_start: 0.8584 (ttp) cc_final: 0.8328 (ttt) REVERT: A 4726 MET cc_start: 0.8435 (tpt) cc_final: 0.7810 (tpp) REVERT: A 4804 MET cc_start: 0.9022 (mmp) cc_final: 0.8725 (mmm) REVERT: E 18 LYS cc_start: 0.9192 (mppt) cc_final: 0.8952 (mppt) REVERT: F 18 LYS cc_start: 0.9110 (mppt) cc_final: 0.8802 (mppt) REVERT: F 58 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8018 (ttpp) REVERT: F 62 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: F 67 MET cc_start: 0.8737 (mtp) cc_final: 0.8463 (mtp) REVERT: G 4 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7437 (mp0) REVERT: G 18 LYS cc_start: 0.9162 (mppt) cc_final: 0.8707 (mppt) REVERT: H 81 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9247 (p) REVERT: B 81 MET cc_start: 0.8293 (tmm) cc_final: 0.7803 (tmm) REVERT: B 661 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9069 (pp) REVERT: B 890 HIS cc_start: 0.9360 (OUTLIER) cc_final: 0.8805 (p-80) REVERT: B 940 LEU cc_start: 0.9494 (mt) cc_final: 0.9258 (pp) REVERT: B 995 MET cc_start: 0.8844 (ttp) cc_final: 0.8307 (ttm) REVERT: B 999 LEU cc_start: 0.9159 (tt) cc_final: 0.8710 (mt) REVERT: B 2485 LEU cc_start: 0.9427 (mm) cc_final: 0.9197 (mm) REVERT: B 2585 MET cc_start: 0.7867 (ppp) cc_final: 0.7619 (ppp) REVERT: B 2734 MET cc_start: 0.9097 (mmp) cc_final: 0.8824 (mmp) REVERT: B 2779 LEU cc_start: 0.9425 (mp) cc_final: 0.9022 (pt) REVERT: B 2840 MET cc_start: 0.9276 (mmm) cc_final: 0.8756 (mmt) REVERT: B 2843 MET cc_start: 0.9075 (ptt) cc_final: 0.8694 (ppp) REVERT: B 2844 MET cc_start: 0.8874 (ppp) cc_final: 0.8511 (ppp) REVERT: B 2893 LEU cc_start: 0.9558 (mp) cc_final: 0.9283 (mm) REVERT: B 2897 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8610 (tm-30) REVERT: B 2921 PHE cc_start: 0.8562 (t80) cc_final: 0.8011 (t80) REVERT: B 2932 TYR cc_start: 0.8251 (t80) cc_final: 0.7916 (t80) REVERT: B 2938 GLN cc_start: 0.8955 (pp30) cc_final: 0.8477 (pp30) REVERT: B 2975 PHE cc_start: 0.8958 (m-80) cc_final: 0.8675 (m-80) REVERT: B 2982 PHE cc_start: 0.8792 (m-80) cc_final: 0.8153 (m-80) REVERT: B 3003 MET cc_start: 0.8642 (ptm) cc_final: 0.8278 (ptm) REVERT: B 3022 PHE cc_start: 0.8017 (m-80) cc_final: 0.7706 (m-80) REVERT: B 3031 ASN cc_start: 0.9144 (t0) cc_final: 0.8799 (t0) REVERT: B 3040 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7447 (mt) REVERT: B 3068 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8885 (pt) REVERT: B 3069 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: B 3105 LEU cc_start: 0.9089 (mt) cc_final: 0.8577 (tt) REVERT: B 3109 PHE cc_start: 0.9292 (m-80) cc_final: 0.8892 (m-80) REVERT: B 3138 TYR cc_start: 0.9291 (t80) cc_final: 0.8940 (t80) REVERT: B 3152 ARG cc_start: 0.8841 (ptp-170) cc_final: 0.8272 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8870 (pp) cc_final: 0.7008 (pp) REVERT: B 3231 MET cc_start: 0.8092 (tmm) cc_final: 0.7841 (tmm) REVERT: B 3241 MET cc_start: 0.9217 (mmp) cc_final: 0.8392 (mmt) REVERT: B 3304 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8613 (tp-100) REVERT: B 3739 MET cc_start: 0.9047 (ttp) cc_final: 0.8748 (ttp) REVERT: B 4672 MET cc_start: 0.8666 (mtm) cc_final: 0.8284 (mtm) REVERT: B 4707 MET cc_start: 0.8589 (ttp) cc_final: 0.8321 (ttt) REVERT: C 81 MET cc_start: 0.8313 (tmm) cc_final: 0.7818 (tmm) REVERT: C 535 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: C 890 HIS cc_start: 0.9301 (OUTLIER) cc_final: 0.8729 (p-80) REVERT: C 895 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8473 (ptt) REVERT: C 940 LEU cc_start: 0.9484 (mt) cc_final: 0.9273 (pp) REVERT: C 995 MET cc_start: 0.8864 (ttp) cc_final: 0.8611 (ttm) REVERT: C 2485 LEU cc_start: 0.9417 (mm) cc_final: 0.9193 (mm) REVERT: C 2734 MET cc_start: 0.9091 (mmp) cc_final: 0.8745 (mmp) REVERT: C 2779 LEU cc_start: 0.9534 (mp) cc_final: 0.9204 (pt) REVERT: C 2840 MET cc_start: 0.9261 (mmt) cc_final: 0.8992 (mmt) REVERT: C 2895 PHE cc_start: 0.9006 (t80) cc_final: 0.8654 (t80) REVERT: C 2897 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8812 (tm-30) REVERT: C 2932 TYR cc_start: 0.8239 (t80) cc_final: 0.7911 (t80) REVERT: C 2938 GLN cc_start: 0.8954 (pp30) cc_final: 0.8484 (pp30) REVERT: C 2975 PHE cc_start: 0.8896 (m-80) cc_final: 0.8622 (m-80) REVERT: C 2982 PHE cc_start: 0.8797 (m-80) cc_final: 0.8196 (m-80) REVERT: C 3003 MET cc_start: 0.8665 (ptm) cc_final: 0.8301 (ptm) REVERT: C 3022 PHE cc_start: 0.7952 (m-80) cc_final: 0.7685 (m-80) REVERT: C 3031 ASN cc_start: 0.9185 (t0) cc_final: 0.8809 (t0) REVERT: C 3040 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7443 (mt) REVERT: C 3068 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8870 (pt) REVERT: C 3069 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: C 3138 TYR cc_start: 0.9249 (t80) cc_final: 0.8936 (t80) REVERT: C 3152 ARG cc_start: 0.8808 (ptp-170) cc_final: 0.8255 (ptp-110) REVERT: C 3159 LEU cc_start: 0.8849 (pp) cc_final: 0.7567 (pp) REVERT: C 3231 MET cc_start: 0.8033 (tmm) cc_final: 0.7774 (tmm) REVERT: C 3241 MET cc_start: 0.9204 (mmp) cc_final: 0.8460 (mmt) REVERT: C 3249 TRP cc_start: 0.8768 (m100) cc_final: 0.8377 (m100) REVERT: C 3302 PHE cc_start: 0.8941 (m-80) cc_final: 0.8735 (m-80) REVERT: C 3304 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8554 (tp-100) REVERT: C 4672 MET cc_start: 0.8610 (mtm) cc_final: 0.8363 (mtm) REVERT: C 4698 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (mt) REVERT: C 4707 MET cc_start: 0.8591 (ttp) cc_final: 0.8250 (ttp) REVERT: C 4726 MET cc_start: 0.8404 (tpt) cc_final: 0.8176 (tpt) REVERT: D 81 MET cc_start: 0.8296 (tmm) cc_final: 0.7805 (tmm) REVERT: D 535 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 655 MET cc_start: 0.8649 (mmm) cc_final: 0.8189 (mmm) REVERT: D 890 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8720 (p-80) REVERT: D 895 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8451 (ptt) REVERT: D 940 LEU cc_start: 0.9479 (mt) cc_final: 0.9262 (pp) REVERT: D 995 MET cc_start: 0.8859 (ttp) cc_final: 0.8598 (ttm) REVERT: D 2485 LEU cc_start: 0.9426 (mm) cc_final: 0.9200 (mm) REVERT: D 2689 MET cc_start: 0.6583 (mtt) cc_final: 0.6016 (mtp) REVERT: D 2734 MET cc_start: 0.9071 (mmp) cc_final: 0.8789 (mmp) REVERT: D 2779 LEU cc_start: 0.9512 (mp) cc_final: 0.9102 (pt) REVERT: D 2843 MET cc_start: 0.8988 (ptp) cc_final: 0.8781 (pmm) REVERT: D 2895 PHE cc_start: 0.8984 (t80) cc_final: 0.8750 (t80) REVERT: D 2897 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8856 (tm-30) REVERT: D 2921 PHE cc_start: 0.8610 (t80) cc_final: 0.8062 (t80) REVERT: D 2932 TYR cc_start: 0.8221 (t80) cc_final: 0.7908 (t80) REVERT: D 2938 GLN cc_start: 0.8928 (pp30) cc_final: 0.8447 (pp30) REVERT: D 2975 PHE cc_start: 0.8927 (m-80) cc_final: 0.8650 (m-80) REVERT: D 2982 PHE cc_start: 0.8792 (m-80) cc_final: 0.8173 (m-80) REVERT: D 3003 MET cc_start: 0.8642 (ptm) cc_final: 0.8273 (ptm) REVERT: D 3031 ASN cc_start: 0.9199 (t0) cc_final: 0.8807 (t0) REVERT: D 3040 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7449 (mt) REVERT: D 3068 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8871 (pt) REVERT: D 3069 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8331 (mm-30) REVERT: D 3138 TYR cc_start: 0.9315 (t80) cc_final: 0.8996 (t80) REVERT: D 3152 ARG cc_start: 0.8836 (ptp-170) cc_final: 0.8303 (ptp-110) REVERT: D 3159 LEU cc_start: 0.8863 (pp) cc_final: 0.7275 (pp) REVERT: D 3231 MET cc_start: 0.8062 (tmm) cc_final: 0.7809 (tmm) REVERT: D 3241 MET cc_start: 0.9219 (mmp) cc_final: 0.8434 (mmt) REVERT: D 3249 TRP cc_start: 0.8762 (m100) cc_final: 0.8364 (m100) REVERT: D 3302 PHE cc_start: 0.8979 (m-80) cc_final: 0.8773 (m-80) REVERT: D 3304 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8622 (tp-100) REVERT: D 4035 TYR cc_start: 0.8200 (m-80) cc_final: 0.7850 (t80) REVERT: D 4046 ARG cc_start: 0.8561 (tpm170) cc_final: 0.8059 (tpp-160) REVERT: D 4672 MET cc_start: 0.8594 (mtm) cc_final: 0.8089 (mtm) REVERT: D 4698 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 4707 MET cc_start: 0.8587 (ttp) cc_final: 0.8253 (ttp) REVERT: D 4726 MET cc_start: 0.8409 (tpt) cc_final: 0.8179 (tpt) REVERT: D 4804 MET cc_start: 0.9033 (mmp) cc_final: 0.8725 (mmm) outliers start: 99 outliers final: 57 residues processed: 1116 average time/residue: 1.1963 time to fit residues: 2360.4044 Evaluate side-chains 1149 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1064 time to evaluate : 11.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 2172 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2172 MET Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2760 TYR Chi-restraints excluded: chain B residue 2980 LEU Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2760 TYR Chi-restraints excluded: chain C residue 2980 LEU Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3686 PHE Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1628 MET Chi-restraints excluded: chain D residue 2234 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2760 TYR Chi-restraints excluded: chain D residue 2980 LEU Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3262 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 4.9990 chunk 1641 optimal weight: 0.7980 chunk 1001 optimal weight: 7.9990 chunk 778 optimal weight: 10.0000 chunk 1140 optimal weight: 9.9990 chunk 1721 optimal weight: 3.9990 chunk 1584 optimal weight: 0.2980 chunk 1370 optimal weight: 0.0000 chunk 142 optimal weight: 8.9990 chunk 1058 optimal weight: 7.9990 chunk 840 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1939 ASN ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN A3955 GLN A3975 GLN A4558 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 GLN B1939 ASN ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 GLN C1939 ASN ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN C4558 HIS ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 GLN D1939 ASN ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4558 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 141728 Z= 0.170 Angle : 0.655 19.979 191492 Z= 0.314 Chirality : 0.041 0.312 20988 Planarity : 0.004 0.127 24600 Dihedral : 5.003 69.123 19108 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 0.57 % Allowed : 8.67 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.07), residues: 17212 helix: 1.75 (0.06), residues: 8892 sheet: 0.11 (0.12), residues: 1680 loop : -0.29 (0.08), residues: 6640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B3249 HIS 0.023 0.001 HIS A3034 PHE 0.040 0.001 PHE A3302 TYR 0.028 0.001 TYR B3245 ARG 0.015 0.000 ARG B1051 ********************** 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 1150 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1063 time to evaluate : 11.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8304 (tmm) cc_final: 0.7827 (tmm) REVERT: A 535 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 655 MET cc_start: 0.8562 (mmm) cc_final: 0.8103 (mmm) REVERT: A 890 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.8760 (p-80) REVERT: A 895 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8441 (ptt) REVERT: A 995 MET cc_start: 0.8829 (ttp) cc_final: 0.8564 (ttm) REVERT: A 2485 LEU cc_start: 0.9407 (mm) cc_final: 0.9178 (mm) REVERT: A 2610 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9080 (mm) REVERT: A 2689 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.4050 (ptt) REVERT: A 2734 MET cc_start: 0.9007 (mmp) cc_final: 0.8674 (mmp) REVERT: A 2779 LEU cc_start: 0.9383 (mp) cc_final: 0.9009 (pt) REVERT: A 2840 MET cc_start: 0.9301 (mmt) cc_final: 0.8484 (mmt) REVERT: A 2843 MET cc_start: 0.8826 (ptp) cc_final: 0.8553 (pmm) REVERT: A 2890 GLN cc_start: 0.8895 (mp10) cc_final: 0.8458 (pm20) REVERT: A 2932 TYR cc_start: 0.8271 (t80) cc_final: 0.7951 (t80) REVERT: A 2938 GLN cc_start: 0.8938 (pp30) cc_final: 0.8468 (pp30) REVERT: A 2975 PHE cc_start: 0.8947 (m-80) cc_final: 0.8675 (m-80) REVERT: A 2982 PHE cc_start: 0.8714 (m-80) cc_final: 0.8096 (m-80) REVERT: A 3003 MET cc_start: 0.8532 (ptm) cc_final: 0.8213 (ptm) REVERT: A 3022 PHE cc_start: 0.7937 (m-80) cc_final: 0.7660 (m-80) REVERT: A 3031 ASN cc_start: 0.9169 (t0) cc_final: 0.8734 (t0) REVERT: A 3040 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7403 (mt) REVERT: A 3068 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8864 (pt) REVERT: A 3069 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: A 3105 LEU cc_start: 0.9041 (mm) cc_final: 0.8478 (tt) REVERT: A 3109 PHE cc_start: 0.9314 (m-10) cc_final: 0.8886 (m-80) REVERT: A 3138 TYR cc_start: 0.9283 (t80) cc_final: 0.8891 (t80) REVERT: A 3152 ARG cc_start: 0.8837 (ptp-170) cc_final: 0.8302 (ptp-110) REVERT: A 3159 LEU cc_start: 0.8868 (pp) cc_final: 0.6968 (pp) REVERT: A 3162 PHE cc_start: 0.8956 (t80) cc_final: 0.8693 (t80) REVERT: A 3241 MET cc_start: 0.9219 (mmp) cc_final: 0.8441 (mmt) REVERT: A 3248 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8123 (ttt180) REVERT: A 3304 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8478 (tp-100) REVERT: A 4035 TYR cc_start: 0.8163 (m-80) cc_final: 0.7896 (t80) REVERT: A 4046 ARG cc_start: 0.8519 (tpm170) cc_final: 0.7914 (tpm170) REVERT: A 4274 MET cc_start: 0.4806 (ttm) cc_final: 0.4122 (mtp) REVERT: A 4672 MET cc_start: 0.8613 (mtm) cc_final: 0.8381 (mtm) REVERT: A 4707 MET cc_start: 0.8562 (ttp) cc_final: 0.8285 (ttt) REVERT: A 4726 MET cc_start: 0.8383 (tpt) cc_final: 0.8162 (tpt) REVERT: A 4804 MET cc_start: 0.8973 (mmp) cc_final: 0.8666 (mmm) REVERT: E 18 LYS cc_start: 0.9192 (mppt) cc_final: 0.8955 (mppt) REVERT: F 58 LYS cc_start: 0.8791 (ttpp) cc_final: 0.7979 (ttpp) REVERT: F 62 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: G 4 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7409 (mp0) REVERT: G 18 LYS cc_start: 0.9167 (mppt) cc_final: 0.8718 (mppt) REVERT: G 74 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8575 (ttpp) REVERT: B 81 MET cc_start: 0.8290 (tmm) cc_final: 0.7804 (tmm) REVERT: B 661 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9063 (pp) REVERT: B 890 HIS cc_start: 0.9296 (OUTLIER) cc_final: 0.8706 (p-80) REVERT: B 895 MET cc_start: 0.9211 (pmm) cc_final: 0.8853 (pmm) REVERT: B 940 LEU cc_start: 0.9488 (mt) cc_final: 0.9246 (pp) REVERT: B 995 MET cc_start: 0.8855 (ttp) cc_final: 0.8308 (ttm) REVERT: B 999 LEU cc_start: 0.9141 (tt) cc_final: 0.8697 (mt) REVERT: B 2485 LEU cc_start: 0.9416 (mm) cc_final: 0.9186 (mm) REVERT: B 2734 MET cc_start: 0.9093 (mmp) cc_final: 0.8850 (mmp) REVERT: B 2779 LEU cc_start: 0.9405 (mp) cc_final: 0.9118 (pt) REVERT: B 2782 MET cc_start: 0.8753 (mmm) cc_final: 0.8528 (mmm) REVERT: B 2893 LEU cc_start: 0.9548 (mp) cc_final: 0.9280 (mm) REVERT: B 2897 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8546 (tm-30) REVERT: B 2932 TYR cc_start: 0.8224 (t80) cc_final: 0.7899 (t80) REVERT: B 2938 GLN cc_start: 0.8930 (pp30) cc_final: 0.8449 (pp30) REVERT: B 2943 PHE cc_start: 0.7693 (m-80) cc_final: 0.7245 (m-80) REVERT: B 2975 PHE cc_start: 0.8906 (m-80) cc_final: 0.8626 (m-80) REVERT: B 2982 PHE cc_start: 0.8725 (m-80) cc_final: 0.8114 (m-80) REVERT: B 3003 MET cc_start: 0.8618 (ptm) cc_final: 0.8266 (ptm) REVERT: B 3022 PHE cc_start: 0.7983 (m-80) cc_final: 0.7661 (m-80) REVERT: B 3031 ASN cc_start: 0.9122 (t0) cc_final: 0.8789 (t0) REVERT: B 3040 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7424 (mt) REVERT: B 3068 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8861 (pt) REVERT: B 3069 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: B 3105 LEU cc_start: 0.9073 (mt) cc_final: 0.8567 (tt) REVERT: B 3109 PHE cc_start: 0.9299 (m-80) cc_final: 0.8883 (m-80) REVERT: B 3138 TYR cc_start: 0.9256 (t80) cc_final: 0.8910 (t80) REVERT: B 3152 ARG cc_start: 0.8830 (ptp-170) cc_final: 0.8287 (ptp-110) REVERT: B 3159 LEU cc_start: 0.8873 (pp) cc_final: 0.7011 (pp) REVERT: B 3241 MET cc_start: 0.9206 (mmp) cc_final: 0.8402 (mmt) REVERT: B 3304 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8575 (tp-100) REVERT: B 4035 TYR cc_start: 0.8183 (m-80) cc_final: 0.7899 (t80) REVERT: B 4046 ARG cc_start: 0.8533 (tpm170) cc_final: 0.7945 (tpm170) REVERT: B 4672 MET cc_start: 0.8648 (mtm) cc_final: 0.8291 (mtm) REVERT: B 4707 MET cc_start: 0.8567 (ttp) cc_final: 0.8299 (ttt) REVERT: B 4726 MET cc_start: 0.8399 (tpt) cc_final: 0.7733 (tpp) REVERT: C 81 MET cc_start: 0.8291 (tmm) cc_final: 0.7796 (tmm) REVERT: C 655 MET cc_start: 0.8584 (mmm) cc_final: 0.8128 (mmm) REVERT: C 890 HIS cc_start: 0.9295 (OUTLIER) cc_final: 0.8715 (p-80) REVERT: C 895 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8441 (ptt) REVERT: C 940 LEU cc_start: 0.9474 (mt) cc_final: 0.9268 (pp) REVERT: C 995 MET cc_start: 0.8843 (ttp) cc_final: 0.8587 (ttm) REVERT: C 2485 LEU cc_start: 0.9405 (mm) cc_final: 0.9184 (mm) REVERT: C 2734 MET cc_start: 0.8897 (mmp) cc_final: 0.8533 (mmp) REVERT: C 2779 LEU cc_start: 0.9548 (mp) cc_final: 0.9286 (pt) REVERT: C 2840 MET cc_start: 0.9162 (mmt) cc_final: 0.8492 (mmt) REVERT: C 2843 MET cc_start: 0.8822 (ptp) cc_final: 0.8584 (pmm) REVERT: C 2895 PHE cc_start: 0.8950 (t80) cc_final: 0.8572 (t80) REVERT: C 2897 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8842 (tm-30) REVERT: C 2932 TYR cc_start: 0.8211 (t80) cc_final: 0.7893 (t80) REVERT: C 2938 GLN cc_start: 0.8932 (pp30) cc_final: 0.8447 (pp30) REVERT: C 2975 PHE cc_start: 0.8882 (m-80) cc_final: 0.8603 (m-80) REVERT: C 2982 PHE cc_start: 0.8751 (m-80) cc_final: 0.8161 (m-80) REVERT: C 3003 MET cc_start: 0.8638 (ptm) cc_final: 0.8359 (ptm) REVERT: C 3022 PHE cc_start: 0.7951 (m-80) cc_final: 0.7712 (m-80) REVERT: C 3031 ASN cc_start: 0.9182 (t0) cc_final: 0.8809 (t0) REVERT: C 3040 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7419 (mt) REVERT: C 3068 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8834 (pt) REVERT: C 3069 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: C 3105 LEU cc_start: 0.9100 (mt) cc_final: 0.8714 (tt) REVERT: C 3138 TYR cc_start: 0.9204 (t80) cc_final: 0.8889 (t80) REVERT: C 3152 ARG cc_start: 0.8800 (ptp-170) cc_final: 0.8263 (ptp-110) REVERT: C 3159 LEU cc_start: 0.8846 (pp) cc_final: 0.7487 (pp) REVERT: C 3241 MET cc_start: 0.9202 (mmp) cc_final: 0.8444 (mmt) REVERT: C 3304 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8516 (tp-100) REVERT: C 4035 TYR cc_start: 0.8181 (m-80) cc_final: 0.7867 (t80) REVERT: C 4046 ARG cc_start: 0.8529 (tpm170) cc_final: 0.7952 (tpm170) REVERT: C 4672 MET cc_start: 0.8615 (mtm) cc_final: 0.8395 (mtm) REVERT: C 4698 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8368 (mt) REVERT: C 4707 MET cc_start: 0.8566 (ttp) cc_final: 0.8219 (ttp) REVERT: C 4726 MET cc_start: 0.8370 (tpt) cc_final: 0.8153 (tpt) REVERT: D 81 MET cc_start: 0.8283 (tmm) cc_final: 0.7782 (tmm) REVERT: D 535 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: D 655 MET cc_start: 0.8555 (mmm) cc_final: 0.8180 (mmm) REVERT: D 890 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.8710 (p-80) REVERT: D 895 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8446 (ptt) REVERT: D 940 LEU cc_start: 0.9475 (mt) cc_final: 0.9254 (pp) REVERT: D 995 MET cc_start: 0.8854 (ttp) cc_final: 0.8596 (ttm) REVERT: D 2485 LEU cc_start: 0.9414 (mm) cc_final: 0.9190 (mm) REVERT: D 2689 MET cc_start: 0.6579 (mtt) cc_final: 0.6019 (mtp) REVERT: D 2734 MET cc_start: 0.9066 (mmp) cc_final: 0.8792 (mmp) REVERT: D 2779 LEU cc_start: 0.9499 (mp) cc_final: 0.9188 (pt) REVERT: D 2843 MET cc_start: 0.8835 (ptp) cc_final: 0.8602 (pmm) REVERT: D 2895 PHE cc_start: 0.8909 (t80) cc_final: 0.8539 (t80) REVERT: D 2897 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8844 (tm-30) REVERT: D 2932 TYR cc_start: 0.8199 (t80) cc_final: 0.7892 (t80) REVERT: D 2938 GLN cc_start: 0.8906 (pp30) cc_final: 0.8409 (pp30) REVERT: D 2975 PHE cc_start: 0.8918 (m-80) cc_final: 0.8634 (m-80) REVERT: D 2982 PHE cc_start: 0.8741 (m-80) cc_final: 0.8107 (m-80) REVERT: D 3003 MET cc_start: 0.8617 (ptm) cc_final: 0.8332 (ptm) REVERT: D 3031 ASN cc_start: 0.9180 (t0) cc_final: 0.8780 (t0) REVERT: D 3040 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7456 (mt) REVERT: D 3068 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8855 (pt) REVERT: D 3069 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: D 3105 LEU cc_start: 0.9073 (mt) cc_final: 0.8719 (tt) REVERT: D 3138 TYR cc_start: 0.9283 (t80) cc_final: 0.8973 (t80) REVERT: D 3152 ARG cc_start: 0.8806 (ptp-170) cc_final: 0.8262 (ptp-110) REVERT: D 3159 LEU cc_start: 0.8862 (pp) cc_final: 0.7260 (pp) REVERT: D 3241 MET cc_start: 0.9200 (mmp) cc_final: 0.8398 (mmt) REVERT: D 3304 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8595 (tp-100) REVERT: D 4035 TYR cc_start: 0.8212 (m-80) cc_final: 0.7904 (t80) REVERT: D 4046 ARG cc_start: 0.8538 (tpm170) cc_final: 0.8030 (tpp-160) REVERT: D 4672 MET cc_start: 0.8574 (mtm) cc_final: 0.8063 (mtm) REVERT: D 4698 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8369 (mt) REVERT: D 4707 MET cc_start: 0.8565 (ttp) cc_final: 0.8231 (ttp) REVERT: D 4726 MET cc_start: 0.8381 (tpt) cc_final: 0.8164 (tpt) outliers start: 87 outliers final: 54 residues processed: 1101 average time/residue: 1.2186 time to fit residues: 2371.1807 Evaluate side-chains 1135 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1054 time to evaluate : 11.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 893 TRP Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 2172 MET Chi-restraints excluded: chain A residue 2234 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 3040 LEU Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4279 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 893 TRP Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2406 MET Chi-restraints excluded: chain B residue 2732 TRP Chi-restraints excluded: chain B residue 2760 TYR Chi-restraints excluded: chain B residue 3040 LEU Chi-restraints excluded: chain B residue 3068 LEU Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3273 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4279 MET Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 893 TRP Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 2406 MET Chi-restraints excluded: chain C residue 2760 TYR Chi-restraints excluded: chain C residue 3040 LEU Chi-restraints excluded: chain C residue 3068 LEU Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3277 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4279 MET Chi-restraints excluded: chain C residue 4698 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 893 TRP Chi-restraints excluded: chain D residue 895 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 2172 MET Chi-restraints excluded: chain D residue 2406 MET Chi-restraints excluded: chain D residue 2585 MET Chi-restraints excluded: chain D residue 2760 TYR Chi-restraints excluded: chain D residue 3040 LEU Chi-restraints excluded: chain D residue 3068 LEU Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 3262 GLU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3686 PHE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4279 MET Chi-restraints excluded: chain D residue 4698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 0.8980 chunk 1460 optimal weight: 0.8980 chunk 419 optimal weight: 7.9990 chunk 1264 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 380 optimal weight: 10.0000 chunk 1373 optimal weight: 6.9990 chunk 574 optimal weight: 1.9990 chunk 1409 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN A4558 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 GLN ** B2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN B4558 HIS ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3955 GLN C3975 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3955 GLN D3975 GLN D4558 HIS D4933 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.053128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.039770 restraints weight = 1178957.341| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.97 r_work: 0.2699 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 141728 Z= 0.267 Angle : 0.666 19.558 191492 Z= 0.322 Chirality : 0.042 0.317 20988 Planarity : 0.004 0.126 24600 Dihedral : 4.969 68.704 19108 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.61 % Allowed : 8.72 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.07), residues: 17212 helix: 1.72 (0.06), residues: 8940 sheet: 0.07 (0.12), residues: 1676 loop : -0.33 (0.08), residues: 6596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B3249 HIS 0.022 0.001 HIS C3034 PHE 0.044 0.001 PHE A3302 TYR 0.038 0.001 TYR A2724 ARG 0.015 0.000 ARG B1051 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44829.14 seconds wall clock time: 779 minutes 57.40 seconds (46797.40 seconds total)