Starting phenix.real_space_refine on Mon Mar 18 18:26:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5i_16437/03_2024/8c5i_16437.pdb" } resolution = 3.15 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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 306 5.16 5 C 29070 2.51 5 N 7380 2.21 5 O 8658 1.98 5 H 43742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 143": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 172": "OD1" <-> "OD2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I ASP 34": "OD1" <-> "OD2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ASP 143": "OD1" <-> "OD2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ASP 172": "OD1" <-> "OD2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 194": "OD1" <-> "OD2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K ASP 143": "OD1" <-> "OD2" Residue "K ASP 172": "OD1" <-> "OD2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "K PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 317": "OE1" <-> "OE2" Residue "K ASP 318": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ASP 172": "OD1" <-> "OD2" Residue "L GLU 181": "OE1" <-> "OE2" Residue "L TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 172": "OD1" <-> "OD2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 107": "OD1" <-> "OD2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N GLU 181": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 143": "OD1" <-> "OD2" Residue "O ASP 172": "OD1" <-> "OD2" Residue "O ASP 254": "OD1" <-> "OD2" Residue "O GLU 259": "OE1" <-> "OE2" Residue "O GLU 271": "OE1" <-> "OE2" Residue "P ASP 107": "OD1" <-> "OD2" Residue "P GLU 195": "OE1" <-> "OE2" Residue "P ASP 232": "OD1" <-> "OD2" Residue "P ASP 269": "OD1" <-> "OD2" Residue "P GLU 317": "OE1" <-> "OE2" Residue "P ASP 318": "OD1" <-> "OD2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 72": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q GLU 181": "OE1" <-> "OE2" Residue "Q TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 318": "OD1" <-> "OD2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R GLU 72": "OE1" <-> "OE2" Residue "R ASP 107": "OD1" <-> "OD2" Residue "R GLU 166": "OE1" <-> "OE2" Residue "R ASP 172": "OD1" <-> "OD2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 194": "OD1" <-> "OD2" Residue "R GLU 229": "OE1" <-> "OE2" Residue "R GLU 261": "OE1" <-> "OE2" Residue "R GLU 271": "OE1" <-> "OE2" Residue "R ASP 318": "OD1" <-> "OD2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "S ASP 143": "OD1" <-> "OD2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ASP 172": "OD1" <-> "OD2" Residue "S ASP 194": "OD1" <-> "OD2" Residue "S GLU 195": "OE1" <-> "OE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 248": "OD1" <-> "OD2" Residue "S ASP 254": "OD1" <-> "OD2" Residue "S GLU 261": "OE1" <-> "OE2" Residue "S TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 89156 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4954 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4954 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4952 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4954 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 4951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4951 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4954 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4955 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4952 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4954 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4952 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4953 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 29.07, per 1000 atoms: 0.33 Number of scatterers: 89156 At special positions: 0 Unit cell: (135.45, 139.65, 215.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 306 16.00 O 8658 8.00 N 7380 7.00 C 29070 6.00 H 43742 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.11 Conformation dependent library (CDL) restraints added in 6.6 seconds 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10728 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 50 sheets defined 36.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.570A pdb=" N GLU A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.548A pdb=" N ALA A 58 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 4.136A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 69 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.730A pdb=" N LEU A 139 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.745A pdb=" N MET A 149 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.826A pdb=" N GLN A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.713A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.794A pdb=" N TYR A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.112A pdb=" N TYR A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 39 removed outlier: 3.635A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.541A pdb=" N ALA B 58 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 4.141A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.578A pdb=" N LEU B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.526A pdb=" N MET B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 149 " --> pdb=" O GLY B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 149' Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.792A pdb=" N MET B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'C' and resid 21 through 38 removed outlier: 3.619A pdb=" N GLU C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.541A pdb=" N ALA C 58 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 4.528A pdb=" N LYS C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE C 69 " --> pdb=" O TYR C 65 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.613A pdb=" N MET C 148 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 149 " --> pdb=" O GLY C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 149' Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.813A pdb=" N GLN C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.563A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'E' and resid 21 through 38 Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.556A pdb=" N ALA E 58 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 4.197A pdb=" N LYS E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE E 69 " --> pdb=" O TYR E 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.794A pdb=" N ARG E 138 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 139 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 149 removed outlier: 3.642A pdb=" N MET E 148 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET E 149 " --> pdb=" O GLY E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 145 through 149' Processing helix chain 'E' and resid 165 through 168 Processing helix chain 'E' and resid 169 through 178 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 217 through 225 removed outlier: 3.784A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET E 223 " --> pdb=" O GLU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 235 Processing helix chain 'E' and resid 273 through 278 removed outlier: 3.507A pdb=" N TYR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.863A pdb=" N ASN F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.506A pdb=" N ILE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 4.567A pdb=" N LYS F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE F 69 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.581A pdb=" N ARG F 138 " --> pdb=" O VAL F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 168 Processing helix chain 'F' and resid 169 through 179 removed outlier: 3.826A pdb=" N GLN F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.690A pdb=" N ARG F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 227 through 235 removed outlier: 3.542A pdb=" N TYR F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.628A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 62 through 76 removed outlier: 4.297A pdb=" N LYS G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE G 69 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 134 through 140 Processing helix chain 'G' and resid 145 through 149 removed outlier: 3.692A pdb=" N MET G 148 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET G 149 " --> pdb=" O GLY G 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 145 through 149' Processing helix chain 'G' and resid 165 through 168 Processing helix chain 'G' and resid 169 through 178 Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 217 through 225 removed outlier: 3.682A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 235 Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'H' and resid 21 through 38 removed outlier: 3.573A pdb=" N GLU H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 removed outlier: 3.560A pdb=" N ALA H 58 " --> pdb=" O PRO H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 76 removed outlier: 4.168A pdb=" N LYS H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU H 72 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 Processing helix chain 'H' and resid 135 through 140 removed outlier: 3.747A pdb=" N ARG H 138 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 139 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 removed outlier: 3.703A pdb=" N MET H 148 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET H 149 " --> pdb=" O GLY H 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 149' Processing helix chain 'H' and resid 165 through 168 Processing helix chain 'H' and resid 169 through 178 Processing helix chain 'H' and resid 194 through 206 Processing helix chain 'H' and resid 217 through 225 removed outlier: 3.591A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 273 through 278 Processing helix chain 'I' and resid 21 through 39 removed outlier: 3.777A pdb=" N ASN I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.507A pdb=" N ALA I 58 " --> pdb=" O PRO I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 removed outlier: 4.332A pdb=" N LYS I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE I 69 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 Processing helix chain 'I' and resid 136 through 140 Processing helix chain 'I' and resid 145 through 149 removed outlier: 3.516A pdb=" N MET I 148 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET I 149 " --> pdb=" O GLY I 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 145 through 149' Processing helix chain 'I' and resid 165 through 168 Processing helix chain 'I' and resid 169 through 179 removed outlier: 3.792A pdb=" N GLN I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 206 removed outlier: 3.892A pdb=" N ARG I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 225 removed outlier: 3.870A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET I 223 " --> pdb=" O GLU I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 235 Processing helix chain 'I' and resid 273 through 278 Processing helix chain 'J' and resid 21 through 38 removed outlier: 3.574A pdb=" N GLU J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.595A pdb=" N ALA J 58 " --> pdb=" O PRO J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 76 removed outlier: 4.170A pdb=" N LYS J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 145 through 149 removed outlier: 3.643A pdb=" N MET J 148 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET J 149 " --> pdb=" O GLY J 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 145 through 149' Processing helix chain 'J' and resid 165 through 168 Processing helix chain 'J' and resid 169 through 179 removed outlier: 3.748A pdb=" N GLN J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 217 through 225 removed outlier: 3.871A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET J 223 " --> pdb=" O GLU J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 235 Processing helix chain 'J' and resid 273 through 278 Processing helix chain 'K' and resid 21 through 39 removed outlier: 3.621A pdb=" N ASN K 39 " --> pdb=" O GLU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.546A pdb=" N ALA K 58 " --> pdb=" O PRO K 55 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 76 removed outlier: 4.197A pdb=" N LYS K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 96 Processing helix chain 'K' and resid 136 through 140 Processing helix chain 'K' and resid 145 through 149 removed outlier: 3.608A pdb=" N MET K 148 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET K 149 " --> pdb=" O GLY K 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 145 through 149' Processing helix chain 'K' and resid 165 through 168 Processing helix chain 'K' and resid 169 through 178 Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'K' and resid 217 through 225 removed outlier: 3.754A pdb=" N MET K 223 " --> pdb=" O GLU K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 235 Processing helix chain 'K' and resid 273 through 278 Processing helix chain 'L' and resid 21 through 39 removed outlier: 3.505A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN L 39 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.511A pdb=" N ILE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 76 removed outlier: 4.038A pdb=" N LYS L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU L 72 " --> pdb=" O LYS L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 165 through 168 Processing helix chain 'L' and resid 169 through 179 removed outlier: 3.821A pdb=" N GLN L 179 " --> pdb=" O ALA L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 217 through 225 removed outlier: 3.533A pdb=" N LYS L 221 " --> pdb=" O THR L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 235 Processing helix chain 'L' and resid 273 through 278 Processing helix chain 'M' and resid 21 through 38 removed outlier: 3.545A pdb=" N GLU M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.603A pdb=" N ALA M 58 " --> pdb=" O PRO M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 76 removed outlier: 4.120A pdb=" N LYS M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 96 Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.540A pdb=" N LEU M 139 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 149 removed outlier: 3.820A pdb=" N MET M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 169 through 179 removed outlier: 3.790A pdb=" N GLN M 179 " --> pdb=" O ALA M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 206 Processing helix chain 'M' and resid 217 through 225 removed outlier: 3.682A pdb=" N LYS M 221 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU M 222 " --> pdb=" O GLU M 218 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 235 removed outlier: 3.802A pdb=" N TYR M 233 " --> pdb=" O GLU M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 277 removed outlier: 4.064A pdb=" N TYR M 276 " --> pdb=" O ARG M 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 39 removed outlier: 3.732A pdb=" N ASN N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 62 through 76 removed outlier: 4.041A pdb=" N LYS N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE N 69 " --> pdb=" O TYR N 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 96 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 145 through 149 removed outlier: 4.029A pdb=" N MET N 149 " --> pdb=" O GLY N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 168 Processing helix chain 'N' and resid 169 through 179 removed outlier: 3.812A pdb=" N GLN N 179 " --> pdb=" O ALA N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 206 Processing helix chain 'N' and resid 217 through 225 Processing helix chain 'N' and resid 227 through 235 Processing helix chain 'N' and resid 273 through 278 Processing helix chain 'O' and resid 21 through 38 removed outlier: 3.722A pdb=" N GLU O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.512A pdb=" N ALA O 58 " --> pdb=" O PRO O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 4.079A pdb=" N LYS O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS O 71 " --> pdb=" O ARG O 67 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS O 75 " --> pdb=" O HIS O 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 96 Processing helix chain 'O' and resid 136 through 140 Processing helix chain 'O' and resid 145 through 149 removed outlier: 3.739A pdb=" N MET O 148 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET O 149 " --> pdb=" O GLY O 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 145 through 149' Processing helix chain 'O' and resid 165 through 168 Processing helix chain 'O' and resid 169 through 178 Processing helix chain 'O' and resid 194 through 206 removed outlier: 3.587A pdb=" N ARG O 199 " --> pdb=" O GLU O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 225 removed outlier: 3.727A pdb=" N LYS O 221 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 222 " --> pdb=" O GLU O 218 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET O 223 " --> pdb=" O GLU O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 235 Processing helix chain 'O' and resid 273 through 278 Processing helix chain 'P' and resid 21 through 39 removed outlier: 3.646A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 62 through 76 removed outlier: 4.699A pdb=" N LYS P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS P 71 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 96 Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.544A pdb=" N LEU P 139 " --> pdb=" O ALA P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 168 Processing helix chain 'P' and resid 169 through 179 removed outlier: 3.799A pdb=" N GLN P 179 " --> pdb=" O ALA P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 206 Processing helix chain 'P' and resid 217 through 225 Processing helix chain 'P' and resid 227 through 235 Processing helix chain 'P' and resid 273 through 278 Processing helix chain 'Q' and resid 21 through 39 removed outlier: 3.847A pdb=" N ASN Q 39 " --> pdb=" O GLU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.503A pdb=" N ILE Q 60 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 76 removed outlier: 4.549A pdb=" N LYS Q 68 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS Q 71 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 96 Processing helix chain 'Q' and resid 134 through 140 Processing helix chain 'Q' and resid 165 through 168 Processing helix chain 'Q' and resid 169 through 179 removed outlier: 3.826A pdb=" N GLN Q 179 " --> pdb=" O ALA Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 206 removed outlier: 3.785A pdb=" N ARG Q 199 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 217 through 225 Processing helix chain 'Q' and resid 227 through 235 removed outlier: 3.567A pdb=" N TYR Q 233 " --> pdb=" O GLU Q 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 278 Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.838A pdb=" N ASN R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 62 through 76 removed outlier: 4.703A pdb=" N LYS R 68 " --> pdb=" O GLU R 64 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 96 Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 145 through 149 removed outlier: 3.928A pdb=" N MET R 149 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 168 Processing helix chain 'R' and resid 169 through 179 removed outlier: 3.851A pdb=" N GLN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 206 removed outlier: 4.628A pdb=" N SER R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 225 Processing helix chain 'R' and resid 227 through 235 Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.971A pdb=" N GLU S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.524A pdb=" N ALA S 58 " --> pdb=" O PRO S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 removed outlier: 4.004A pdb=" N LYS S 68 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS S 71 " --> pdb=" O ARG S 67 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU S 72 " --> pdb=" O LYS S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 96 Processing helix chain 'S' and resid 134 through 140 Processing helix chain 'S' and resid 145 through 149 removed outlier: 3.740A pdb=" N MET S 149 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 168 Processing helix chain 'S' and resid 169 through 178 removed outlier: 3.508A pdb=" N LEU S 173 " --> pdb=" O VAL S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 206 removed outlier: 3.612A pdb=" N ILE S 203 " --> pdb=" O ARG S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 217 through 225 removed outlier: 3.822A pdb=" N LYS S 221 " --> pdb=" O THR S 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU S 222 " --> pdb=" O GLU S 218 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET S 223 " --> pdb=" O GLU S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 234 removed outlier: 3.557A pdb=" N TYR S 233 " --> pdb=" O GLU S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 237 No H-bonds generated for 'chain 'S' and resid 235 through 237' Processing helix chain 'S' and resid 273 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 129 removed outlier: 3.944A pdb=" N GLY A 126 " --> pdb=" O TRP A 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 43 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA3, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 129 removed outlier: 3.841A pdb=" N GLY B 126 " --> pdb=" O TRP B 117 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B 110 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 removed outlier: 3.544A pdb=" N GLY B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 185 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER B 187 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 162 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 306 Processing sheet with id=AA7, first strand: chain 'C' and resid 124 through 129 removed outlier: 3.920A pdb=" N GLY C 126 " --> pdb=" O TRP C 117 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 43 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.277A pdb=" N ASN C 158 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL C 185 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY C 160 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 187 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 162 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 124 through 129 removed outlier: 3.801A pdb=" N GLY E 126 " --> pdb=" O TRP E 117 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 43 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.569A pdb=" N GLY E 157 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN E 158 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL E 185 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY E 160 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER E 187 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E 162 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 303 through 306 removed outlier: 8.683A pdb=" N LYS O 304 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET E 293 " --> pdb=" O LYS O 304 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU O 306 " --> pdb=" O MET E 293 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE E 295 " --> pdb=" O LEU O 306 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LYS S 304 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET G 293 " --> pdb=" O LYS S 304 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU S 306 " --> pdb=" O MET G 293 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE G 295 " --> pdb=" O LEU S 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 124 through 129 removed outlier: 3.946A pdb=" N GLY F 126 " --> pdb=" O TRP F 117 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER F 110 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL F 44 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER F 102 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 43 " --> pdb=" O ARG F 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AB5, first strand: chain 'F' and resid 161 through 163 removed outlier: 6.650A pdb=" N LEU F 162 " --> pdb=" O SER F 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 303 through 306 removed outlier: 6.417A pdb=" N LYS F 304 " --> pdb=" O PHE P 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 124 through 129 removed outlier: 3.866A pdb=" N GLY G 126 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G 43 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 152 through 154 removed outlier: 3.649A pdb=" N GLY G 157 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN G 158 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL G 185 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY G 160 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N SER G 187 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU G 162 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 303 through 306 removed outlier: 6.487A pdb=" N LYS I 304 " --> pdb=" O PHE O 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 124 through 129 removed outlier: 3.790A pdb=" N GLY H 126 " --> pdb=" O TRP H 117 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU H 43 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 152 through 154 removed outlier: 6.120A pdb=" N ASN H 158 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL H 185 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY H 160 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER H 187 " --> pdb=" O GLY H 160 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU H 162 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 303 through 306 removed outlier: 6.363A pdb=" N LYS H 304 " --> pdb=" O PHE J 295 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N LYS K 304 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET I 293 " --> pdb=" O LYS K 304 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU K 306 " --> pdb=" O MET I 293 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE I 295 " --> pdb=" O LEU K 306 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 124 through 129 removed outlier: 3.838A pdb=" N GLY I 126 " --> pdb=" O TRP I 117 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL I 44 " --> pdb=" O CYS I 100 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N SER I 102 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 43 " --> pdb=" O ARG I 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 152 through 154 removed outlier: 6.311A pdb=" N ASN I 158 " --> pdb=" O VAL I 183 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL I 185 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY I 160 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER I 187 " --> pdb=" O GLY I 160 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU I 162 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 124 through 129 removed outlier: 3.898A pdb=" N GLY J 126 " --> pdb=" O TRP J 117 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 99 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU J 43 " --> pdb=" O ARG J 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 152 through 154 removed outlier: 6.272A pdb=" N ASN J 158 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL J 185 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY J 160 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER J 187 " --> pdb=" O GLY J 160 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU J 162 " --> pdb=" O SER J 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 303 through 306 removed outlier: 6.384A pdb=" N LYS J 304 " --> pdb=" O PHE M 295 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LYS N 304 " --> pdb=" O LEU K 291 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET K 293 " --> pdb=" O LYS N 304 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU N 306 " --> pdb=" O MET K 293 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE K 295 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 124 through 129 removed outlier: 3.863A pdb=" N GLY K 126 " --> pdb=" O TRP K 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 43 " --> pdb=" O ARG K 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 152 through 154 removed outlier: 3.507A pdb=" N GLY K 157 " --> pdb=" O THR K 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 124 through 129 removed outlier: 3.926A pdb=" N GLY L 126 " --> pdb=" O TRP L 117 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL L 99 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL L 44 " --> pdb=" O CYS L 100 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER L 102 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU L 43 " --> pdb=" O ARG L 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 152 through 154 Processing sheet with id=AD4, first strand: chain 'L' and resid 293 through 296 Processing sheet with id=AD5, first strand: chain 'M' and resid 124 through 129 removed outlier: 3.948A pdb=" N GLY M 126 " --> pdb=" O TRP M 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 152 through 154 Processing sheet with id=AD7, first strand: chain 'N' and resid 124 through 129 removed outlier: 3.989A pdb=" N GLY N 126 " --> pdb=" O TRP N 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU N 43 " --> pdb=" O ARG N 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 152 through 154 Processing sheet with id=AD9, first strand: chain 'N' and resid 293 through 296 Processing sheet with id=AE1, first strand: chain 'O' and resid 124 through 129 removed outlier: 3.857A pdb=" N GLY O 126 " --> pdb=" O TRP O 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU O 43 " --> pdb=" O ARG O 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 152 through 154 removed outlier: 3.657A pdb=" N GLY O 157 " --> pdb=" O THR O 154 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN O 158 " --> pdb=" O VAL O 183 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL O 185 " --> pdb=" O ASN O 158 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY O 160 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER O 187 " --> pdb=" O GLY O 160 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU O 162 " --> pdb=" O SER O 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 124 through 129 removed outlier: 3.912A pdb=" N GLY P 126 " --> pdb=" O TRP P 117 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL P 99 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL P 44 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER P 102 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 152 through 154 removed outlier: 3.616A pdb=" N GLY P 157 " --> pdb=" O THR P 154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 161 through 162 removed outlier: 3.674A pdb=" N ALA P 186 " --> pdb=" O LEU P 210 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 124 through 129 removed outlier: 3.919A pdb=" N GLY Q 126 " --> pdb=" O TRP Q 117 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER Q 110 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL Q 44 " --> pdb=" O CYS Q 100 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N SER Q 102 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 152 through 154 Processing sheet with id=AE8, first strand: chain 'Q' and resid 161 through 163 removed outlier: 6.678A pdb=" N LEU Q 162 " --> pdb=" O SER Q 187 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 303 through 306 removed outlier: 6.392A pdb=" N LYS Q 304 " --> pdb=" O PHE R 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'R' and resid 124 through 129 removed outlier: 3.921A pdb=" N GLY R 126 " --> pdb=" O TRP R 117 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL R 44 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER R 102 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU R 43 " --> pdb=" O ARG R 9 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 152 through 154 removed outlier: 3.674A pdb=" N GLY R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 161 through 163 removed outlier: 6.645A pdb=" N LEU R 162 " --> pdb=" O SER R 187 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 124 through 129 removed outlier: 3.835A pdb=" N GLY S 126 " --> pdb=" O TRP S 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 152 through 154 removed outlier: 3.731A pdb=" N GLY S 157 " --> pdb=" O THR S 154 " (cutoff:3.500A) 1802 hydrogen bonds defined for protein. 4908 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: 39.40 Time building geometry restraints manager: 57.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 43634 1.03 - 1.23: 143 1.23 - 1.42: 20215 1.42 - 1.62: 25866 1.62 - 1.81: 504 Bond restraints: 90362 Sorted by residual: bond pdb=" C ALA O 45 " pdb=" N PHE O 46 " ideal model delta sigma weight residual 1.331 1.379 -0.048 1.59e-02 3.96e+03 9.10e+00 bond pdb=" C ALA H 45 " pdb=" N PHE H 46 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.59e-02 3.96e+03 7.88e+00 bond pdb=" C ALA E 45 " pdb=" N PHE E 46 " ideal model delta sigma weight residual 1.331 1.375 -0.044 1.59e-02 3.96e+03 7.54e+00 bond pdb=" C PHE B 118 " pdb=" N ASN B 119 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.59e-02 3.96e+03 5.64e+00 bond pdb=" N SER B 3 " pdb=" CA SER B 3 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.37e+00 ... (remaining 90357 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 1814 106.89 - 113.67: 104823 113.67 - 120.45: 30133 120.45 - 127.23: 25502 127.23 - 134.01: 596 Bond angle restraints: 162868 Sorted by residual: angle pdb=" C CYS N 164 " pdb=" CA CYS N 164 " pdb=" CB CYS N 164 " ideal model delta sigma weight residual 116.54 110.92 5.62 1.15e+00 7.56e-01 2.39e+01 angle pdb=" C CYS E 164 " pdb=" CA CYS E 164 " pdb=" CB CYS E 164 " ideal model delta sigma weight residual 116.54 111.06 5.48 1.15e+00 7.56e-01 2.27e+01 angle pdb=" C CYS B 164 " pdb=" CA CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sigma weight residual 116.54 111.09 5.45 1.15e+00 7.56e-01 2.24e+01 angle pdb=" C CYS H 164 " pdb=" CA CYS H 164 " pdb=" CB CYS H 164 " ideal model delta sigma weight residual 116.54 111.13 5.41 1.15e+00 7.56e-01 2.21e+01 angle pdb=" C CYS K 164 " pdb=" CA CYS K 164 " pdb=" CB CYS K 164 " ideal model delta sigma weight residual 116.54 111.16 5.38 1.15e+00 7.56e-01 2.19e+01 ... (remaining 162863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 38603 17.96 - 35.92: 3207 35.92 - 53.87: 1097 53.87 - 71.83: 238 71.83 - 89.79: 111 Dihedral angle restraints: 43256 sinusoidal: 22806 harmonic: 20450 Sorted by residual: dihedral pdb=" CA VAL Q 256 " pdb=" C VAL Q 256 " pdb=" N PRO Q 257 " pdb=" CA PRO Q 257 " ideal model delta harmonic sigma weight residual -180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE K 46 " pdb=" C PHE K 46 " pdb=" N PRO K 47 " pdb=" CA PRO K 47 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL I 256 " pdb=" C VAL I 256 " pdb=" N PRO I 257 " pdb=" CA PRO I 257 " ideal model delta harmonic sigma weight residual -180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 43253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4340 0.033 - 0.067: 1685 0.067 - 0.100: 257 0.100 - 0.133: 341 0.133 - 0.167: 37 Chirality restraints: 6660 Sorted by residual: chirality pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" C PRO B 47 " pdb=" CB PRO B 47 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA PRO K 47 " pdb=" N PRO K 47 " pdb=" C PRO K 47 " pdb=" CB PRO K 47 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA PRO P 47 " pdb=" N PRO P 47 " pdb=" C PRO P 47 " pdb=" CB PRO P 47 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 6657 not shown) Planarity restraints: 13608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN N 119 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO N 120 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO N 120 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 120 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 188 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO R 189 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 189 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 189 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 188 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C 189 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 189 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 189 " -0.027 5.00e-02 4.00e+02 ... (remaining 13605 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2851 2.16 - 2.77: 169267 2.77 - 3.38: 243880 3.38 - 3.99: 332206 3.99 - 4.60: 523966 Nonbonded interactions: 1272170 Sorted by model distance: nonbonded pdb=" O ASN B 119 " pdb=" H GLY B 122 " model vdw 1.551 1.850 nonbonded pdb=" HH TYR E 54 " pdb=" OE2 GLU E 137 " model vdw 1.573 1.850 nonbonded pdb=" HH TYR S 54 " pdb=" OE2 GLU S 137 " model vdw 1.577 1.850 nonbonded pdb=" HH TYR H 54 " pdb=" OE2 GLU H 137 " model vdw 1.577 1.850 nonbonded pdb=" HH TYR G 54 " pdb=" OE2 GLU G 137 " model vdw 1.579 1.850 ... (remaining 1272165 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 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'B' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'C' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'E' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 242 through 319)) selection = (chain 'F' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 242 through 319)) selection = (chain 'G' and (resid 3 through 240 or (resid 241 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 242 through 319)) selection = (chain 'H' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 242 through 319)) selection = chain 'I' selection = (chain 'J' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'K' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'L' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 284 or (resid 285 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 286 through 319)) selection = (chain 'M' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) selection = (chain 'N' and (resid 3 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 72 through 166 or (resid 167 and (name N or name CA or name C or na \ me O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or na \ me H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or \ resid 168 through 183 or (resid 184 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resi \ d 185 through 284 or (resid 285 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 286 \ through 319)) selection = (chain 'O' and (resid 3 through 183 or (resid 184 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 185 through 240 or (resid 241 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 242 through 319)) selection = (chain 'P' and (resid 3 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 286 through 319)) selection = (chain 'Q' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 242 through 319)) selection = (chain 'R' and (resid 3 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 286 through 319)) selection = (chain 'S' and (resid 3 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 168 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 185 through 319)) } 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=1.00 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.080 Extract box with map and model: 9.330 Check model and map are aligned: 1.000 Set scattering table: 0.610 Process input model: 217.260 Find NCS groups from input model: 4.140 Set up NCS constraints: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46620 Z= 0.241 Angle : 0.559 6.145 63252 Z= 0.320 Chirality : 0.042 0.167 6660 Planarity : 0.004 0.056 8226 Dihedral : 16.202 89.791 17064 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.06 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 14.06 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.11), residues: 5670 helix: -0.15 (0.13), residues: 1620 sheet: 0.52 (0.15), residues: 1206 loop : -1.49 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.008 0.001 PHE B 118 TYR 0.013 0.001 TYR I 278 ARG 0.002 0.000 ARG S 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 453 time to evaluate : 5.359 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: G 119 ASN cc_start: 0.8809 (m-40) cc_final: 0.8570 (t0) REVERT: I 228 GLN cc_start: 0.7582 (tp40) cc_final: 0.7318 (tp-100) REVERT: L 228 GLN cc_start: 0.7417 (tp40) cc_final: 0.7054 (mm110) REVERT: S 34 ASP cc_start: 0.8102 (m-30) cc_final: 0.7790 (m-30) outliers start: 6 outliers final: 5 residues processed: 457 average time/residue: 1.1667 time to fit residues: 870.6493 Evaluate side-chains 448 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 443 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain Q residue 313 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 471 optimal weight: 5.9990 chunk 422 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 437 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 325 optimal weight: 4.9990 chunk 506 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 62 HIS ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 HIS R 184 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46620 Z= 0.279 Angle : 0.552 10.391 63252 Z= 0.296 Chirality : 0.044 0.172 6660 Planarity : 0.004 0.068 8226 Dihedral : 5.279 25.717 6236 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.81 % Favored : 94.80 % Rotamer: Outliers : 0.87 % Allowed : 13.90 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.02 (0.11), residues: 5670 helix: -0.07 (0.13), residues: 1656 sheet: 0.45 (0.15), residues: 1206 loop : -1.57 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 188 HIS 0.005 0.001 HIS S 62 PHE 0.010 0.001 PHE I 208 TYR 0.015 0.001 TYR S 278 ARG 0.003 0.000 ARG I 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 463 time to evaluate : 5.255 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: E 194 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8503 (p0) REVERT: L 105 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: P 228 GLN cc_start: 0.7285 (tp-100) cc_final: 0.7055 (mm110) outliers start: 42 outliers final: 29 residues processed: 487 average time/residue: 1.1671 time to fit residues: 923.8097 Evaluate side-chains 468 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 437 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 281 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 421 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 507 optimal weight: 5.9990 chunk 548 optimal weight: 6.9990 chunk 452 optimal weight: 6.9990 chunk 503 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 407 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN E 307 ASN I 228 GLN ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 46620 Z= 0.278 Angle : 0.536 9.178 63252 Z= 0.286 Chirality : 0.043 0.178 6660 Planarity : 0.004 0.069 8226 Dihedral : 5.260 26.858 6232 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.04 % Favored : 94.57 % Rotamer: Outliers : 1.36 % Allowed : 13.55 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.94 (0.11), residues: 5670 helix: 0.01 (0.13), residues: 1656 sheet: 0.40 (0.14), residues: 1296 loop : -1.54 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 188 HIS 0.004 0.001 HIS R 184 PHE 0.009 0.001 PHE P 118 TYR 0.011 0.001 TYR S 278 ARG 0.003 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 448 time to evaluate : 5.358 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: A 75 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: E 194 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8500 (p0) REVERT: H 194 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8498 (p0) REVERT: K 261 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7068 (tm-30) REVERT: L 132 ARG cc_start: 0.5755 (mtt180) cc_final: 0.5507 (mtt180) REVERT: P 228 GLN cc_start: 0.7277 (tp-100) cc_final: 0.7059 (mm110) REVERT: P 294 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8467 (m-40) REVERT: Q 211 MET cc_start: 0.8916 (ttp) cc_final: 0.8710 (ttm) REVERT: R 228 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7038 (mm110) REVERT: S 155 GLU cc_start: 0.8076 (mp0) cc_final: 0.7725 (mp0) outliers start: 66 outliers final: 46 residues processed: 490 average time/residue: 1.1625 time to fit residues: 932.5201 Evaluate side-chains 490 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 440 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 220 MET Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 501 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 509 optimal weight: 0.7980 chunk 539 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 482 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 ASN I 228 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN S 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 46620 Z= 0.261 Angle : 0.528 9.007 63252 Z= 0.281 Chirality : 0.043 0.175 6660 Planarity : 0.004 0.069 8226 Dihedral : 5.232 28.036 6232 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.20 % Favored : 94.41 % Rotamer: Outliers : 1.59 % Allowed : 13.61 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.93 (0.11), residues: 5670 helix: 0.05 (0.13), residues: 1656 sheet: 0.38 (0.14), residues: 1296 loop : -1.54 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.008 0.001 PHE L 118 TYR 0.011 0.001 TYR K 276 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 451 time to evaluate : 5.447 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: A 75 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8586 (mttp) REVERT: E 194 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8506 (p0) REVERT: G 32 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8199 (tp) REVERT: H 194 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8473 (p0) REVERT: L 132 ARG cc_start: 0.5832 (mtt180) cc_final: 0.5578 (mtt180) REVERT: P 228 GLN cc_start: 0.7262 (tp-100) cc_final: 0.7047 (mm110) REVERT: P 294 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8466 (m-40) REVERT: R 228 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7025 (mm110) REVERT: S 34 ASP cc_start: 0.8208 (m-30) cc_final: 0.7757 (m-30) outliers start: 77 outliers final: 57 residues processed: 502 average time/residue: 1.1426 time to fit residues: 939.5791 Evaluate side-chains 503 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 441 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 292 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain L residue 294 ASN Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 449 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 460 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 484 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN S 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 46620 Z= 0.295 Angle : 0.538 8.931 63252 Z= 0.286 Chirality : 0.044 0.180 6660 Planarity : 0.004 0.070 8226 Dihedral : 5.274 27.444 6232 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.43 % Favored : 94.18 % Rotamer: Outliers : 1.78 % Allowed : 13.88 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.97 (0.11), residues: 5670 helix: 0.03 (0.13), residues: 1656 sheet: 0.34 (0.14), residues: 1296 loop : -1.58 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.009 0.001 PHE L 118 TYR 0.011 0.001 TYR B 276 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 458 time to evaluate : 5.338 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: A 75 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8587 (mttp) REVERT: E 194 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8460 (p0) REVERT: G 32 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8156 (tp) REVERT: H 194 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8436 (p0) REVERT: L 132 ARG cc_start: 0.5839 (mtt180) cc_final: 0.5567 (mtt180) REVERT: P 228 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7042 (mm110) REVERT: P 294 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8479 (m-40) REVERT: Q 132 ARG cc_start: 0.6321 (ttp-170) cc_final: 0.3684 (ttm170) REVERT: Q 211 MET cc_start: 0.8911 (ttp) cc_final: 0.8700 (ttm) REVERT: R 228 GLN cc_start: 0.7273 (tp-100) cc_final: 0.7024 (mm110) REVERT: S 34 ASP cc_start: 0.8223 (m-30) cc_final: 0.7779 (m-30) outliers start: 86 outliers final: 68 residues processed: 519 average time/residue: 1.2312 time to fit residues: 1058.2293 Evaluate side-chains 521 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 448 time to evaluate : 5.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 292 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain L residue 294 ASN Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 280 ILE Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 294 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 181 optimal weight: 6.9990 chunk 485 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 539 optimal weight: 6.9990 chunk 448 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 115 GLN S 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46620 Z= 0.293 Angle : 0.537 8.826 63252 Z= 0.285 Chirality : 0.043 0.180 6660 Planarity : 0.004 0.069 8226 Dihedral : 5.286 30.364 6232 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.43 % Favored : 94.18 % Rotamer: Outliers : 1.92 % Allowed : 13.88 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.11), residues: 5670 helix: 0.01 (0.13), residues: 1656 sheet: 0.34 (0.14), residues: 1296 loop : -1.59 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.009 0.001 PHE L 118 TYR 0.011 0.001 TYR B 276 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 453 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: E 194 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8455 (p0) REVERT: F 86 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7161 (mtt90) REVERT: G 32 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8151 (tp) REVERT: H 194 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8437 (p0) REVERT: K 261 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7093 (tm-30) REVERT: L 48 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: L 132 ARG cc_start: 0.5818 (mtt180) cc_final: 0.5533 (mtt180) REVERT: P 228 GLN cc_start: 0.7269 (tp-100) cc_final: 0.7038 (mm110) REVERT: P 294 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: Q 132 ARG cc_start: 0.6331 (ttp-170) cc_final: 0.5223 (tmm160) REVERT: Q 306 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (mt) REVERT: R 228 GLN cc_start: 0.7271 (tp-100) cc_final: 0.7022 (mm110) REVERT: S 34 ASP cc_start: 0.8254 (m-30) cc_final: 0.7799 (m-30) outliers start: 93 outliers final: 78 residues processed: 522 average time/residue: 1.1621 time to fit residues: 989.8486 Evaluate side-chains 540 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 455 time to evaluate : 5.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 292 SER Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 294 ASN Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 280 ILE Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 294 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 306 LEU Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 115 GLN Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 520 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 307 optimal weight: 7.9990 chunk 394 optimal weight: 0.8980 chunk 305 optimal weight: 7.9990 chunk 454 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 537 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 228 GLN ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN S 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 46620 Z= 0.251 Angle : 0.525 8.469 63252 Z= 0.279 Chirality : 0.043 0.179 6660 Planarity : 0.004 0.068 8226 Dihedral : 5.234 30.496 6232 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.34 % Favored : 94.27 % Rotamer: Outliers : 2.04 % Allowed : 13.82 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5670 helix: 0.06 (0.13), residues: 1656 sheet: 0.36 (0.14), residues: 1296 loop : -1.58 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.008 0.001 PHE L 118 TYR 0.010 0.001 TYR B 276 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 464 time to evaluate : 5.377 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: A 75 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (mttp) REVERT: E 194 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8444 (p0) REVERT: F 86 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7065 (mtt90) REVERT: G 32 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8188 (tp) REVERT: H 194 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8433 (p0) REVERT: L 48 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: L 132 ARG cc_start: 0.5879 (mtt180) cc_final: 0.5611 (mtt180) REVERT: P 228 GLN cc_start: 0.7263 (tp-100) cc_final: 0.7036 (mm110) REVERT: P 294 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8476 (m-40) REVERT: Q 48 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: Q 132 ARG cc_start: 0.6335 (ttp-170) cc_final: 0.5218 (tmm160) REVERT: Q 211 MET cc_start: 0.8916 (ttp) cc_final: 0.8693 (ttm) REVERT: R 228 GLN cc_start: 0.7265 (tp-100) cc_final: 0.7018 (mm110) REVERT: S 34 ASP cc_start: 0.8255 (m-30) cc_final: 0.7794 (m-30) outliers start: 99 outliers final: 83 residues processed: 536 average time/residue: 1.1552 time to fit residues: 1008.0659 Evaluate side-chains 544 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 454 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 220 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 292 SER Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain K residue 313 VAL Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 294 ASN Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain M residue 280 ILE Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 223 MET Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 280 ILE Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 294 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 312 GLU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 211 MET Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 332 optimal weight: 0.6980 chunk 214 optimal weight: 0.0980 chunk 321 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 366 optimal weight: 0.0020 chunk 265 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 422 optimal weight: 4.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 294 ASN ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 46620 Z= 0.132 Angle : 0.480 7.093 63252 Z= 0.254 Chirality : 0.042 0.147 6660 Planarity : 0.004 0.062 8226 Dihedral : 4.892 29.012 6232 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.07 % Favored : 95.56 % Rotamer: Outliers : 0.99 % Allowed : 14.79 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.71 (0.11), residues: 5670 helix: 0.39 (0.13), residues: 1638 sheet: 0.45 (0.14), residues: 1296 loop : -1.49 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 188 HIS 0.002 0.001 HIS B 167 PHE 0.006 0.001 PHE L 118 TYR 0.010 0.001 TYR Q 276 ARG 0.002 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 490 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8550 (mttp) REVERT: B 131 MET cc_start: 0.8751 (mmm) cc_final: 0.8465 (mmm) REVERT: E 194 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8490 (p0) REVERT: H 194 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8483 (p0) REVERT: M 67 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.7136 (mmp-170) REVERT: P 228 GLN cc_start: 0.7244 (tp-100) cc_final: 0.7032 (mm110) REVERT: Q 211 MET cc_start: 0.8905 (ttp) cc_final: 0.8680 (ttm) REVERT: Q 306 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8593 (mt) REVERT: R 228 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6983 (mm110) REVERT: S 155 GLU cc_start: 0.7964 (mp0) cc_final: 0.7537 (mp0) outliers start: 48 outliers final: 39 residues processed: 524 average time/residue: 1.1383 time to fit residues: 976.5603 Evaluate side-chains 502 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 459 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 280 ILE Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 306 LEU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 489 optimal weight: 3.9990 chunk 515 optimal weight: 7.9990 chunk 470 optimal weight: 0.9990 chunk 501 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 393 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 452 optimal weight: 6.9990 chunk 474 optimal weight: 4.9990 chunk 499 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 GLN ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 46620 Z= 0.140 Angle : 0.482 8.310 63252 Z= 0.254 Chirality : 0.042 0.152 6660 Planarity : 0.004 0.062 8226 Dihedral : 4.826 28.118 6232 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.22 % Favored : 95.41 % Rotamer: Outliers : 0.97 % Allowed : 14.91 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.65 (0.11), residues: 5670 helix: 0.46 (0.13), residues: 1638 sheet: 0.48 (0.14), residues: 1296 loop : -1.47 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 188 HIS 0.003 0.001 HIS F 128 PHE 0.007 0.001 PHE A 295 TYR 0.009 0.001 TYR Q 276 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 457 time to evaluate : 5.493 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: A 75 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: B 131 MET cc_start: 0.8763 (mmm) cc_final: 0.8482 (mmm) REVERT: E 194 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8496 (p0) REVERT: H 194 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8514 (p0) REVERT: K 176 MET cc_start: 0.8951 (mmm) cc_final: 0.8238 (mmt) REVERT: M 67 ARG cc_start: 0.7499 (mmp-170) cc_final: 0.7128 (mmp-170) REVERT: P 228 GLN cc_start: 0.7243 (tp-100) cc_final: 0.7031 (mm110) REVERT: Q 48 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: Q 211 MET cc_start: 0.8900 (ttp) cc_final: 0.8675 (ttm) REVERT: Q 306 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8611 (mt) REVERT: R 228 GLN cc_start: 0.7226 (tp-100) cc_final: 0.6994 (mm110) REVERT: S 155 GLU cc_start: 0.7965 (mp0) cc_final: 0.7528 (mp0) outliers start: 47 outliers final: 39 residues processed: 490 average time/residue: 1.1594 time to fit residues: 932.9817 Evaluate side-chains 497 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 453 time to evaluate : 5.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 306 LEU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 329 optimal weight: 4.9990 chunk 529 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 368 optimal weight: 0.6980 chunk 555 optimal weight: 5.9990 chunk 511 optimal weight: 5.9990 chunk 442 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 46620 Z= 0.321 Angle : 0.548 9.723 63252 Z= 0.290 Chirality : 0.044 0.187 6660 Planarity : 0.005 0.069 8226 Dihedral : 5.142 30.628 6232 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.68 % Favored : 93.95 % Rotamer: Outliers : 1.16 % Allowed : 14.87 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.84 (0.11), residues: 5670 helix: 0.25 (0.13), residues: 1620 sheet: 0.40 (0.14), residues: 1296 loop : -1.54 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 188 HIS 0.004 0.001 HIS B 71 PHE 0.011 0.001 PHE R 57 TYR 0.012 0.001 TYR B 276 ARG 0.004 0.000 ARG B 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11340 Ramachandran restraints generated. 5670 Oldfield, 0 Emsley, 5670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 450 time to evaluate : 5.405 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: A 75 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: E 194 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8444 (p0) REVERT: F 86 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7048 (mtt90) REVERT: F 163 MET cc_start: 0.8984 (mtm) cc_final: 0.8765 (mtm) REVERT: H 194 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8455 (p0) REVERT: H 222 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7512 (mm-30) REVERT: M 67 ARG cc_start: 0.7553 (mmp-170) cc_final: 0.7188 (mmp-170) REVERT: P 228 GLN cc_start: 0.7257 (tp-100) cc_final: 0.7030 (mm110) REVERT: P 294 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8477 (m-40) REVERT: Q 132 ARG cc_start: 0.6422 (ttp-170) cc_final: 0.5268 (tmm160) REVERT: Q 211 MET cc_start: 0.8939 (ttp) cc_final: 0.8720 (ttm) REVERT: Q 306 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8605 (mt) REVERT: R 228 GLN cc_start: 0.7245 (tp-100) cc_final: 0.6991 (mm110) outliers start: 56 outliers final: 45 residues processed: 488 average time/residue: 1.1575 time to fit residues: 918.6150 Evaluate side-chains 498 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 448 time to evaluate : 5.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 298 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 292 SER Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 194 ASP Chi-restraints excluded: chain M residue 211 MET Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain O residue 292 SER Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain P residue 294 ASN Chi-restraints excluded: chain P residue 313 VAL Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 306 LEU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain S residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 351 optimal weight: 4.9990 chunk 471 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 408 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 443 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098243 restraints weight = 173127.450| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.45 r_work: 0.3010 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46620 Z= 0.226 Angle : 0.513 9.443 63252 Z= 0.271 Chirality : 0.043 0.171 6660 Planarity : 0.004 0.068 8226 Dihedral : 5.082 31.187 6232 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.96 % Favored : 94.67 % Rotamer: Outliers : 1.07 % Allowed : 14.91 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.11), residues: 5670 helix: 0.28 (0.13), residues: 1638 sheet: 0.40 (0.14), residues: 1296 loop : -1.55 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 188 HIS 0.003 0.001 HIS B 71 PHE 0.008 0.001 PHE L 118 TYR 0.010 0.001 TYR F 276 ARG 0.003 0.000 ARG B 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17098.16 seconds wall clock time: 298 minutes 2.10 seconds (17882.10 seconds total)