Starting phenix.real_space_refine on Sun Feb 25 07:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsd_33524/02_2024/7xsd_33524.pdb" } resolution = 3.3 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= 0.004 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 31592 2.51 5 N 8824 2.21 5 O 9264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 ARG 102": "NH1" <-> "NH2" Residue "6 ARG 74": "NH1" <-> "NH2" Residue "7 ARG 61": "NH1" <-> "NH2" Residue "7 ARG 102": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 160": "NH1" <-> "NH2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 214": "NH1" <-> "NH2" Residue "H ARG 218": "NH1" <-> "NH2" Residue "H ARG 254": "NH1" <-> "NH2" Residue "H PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 61": "NH1" <-> "NH2" Residue "1 ARG 102": "NH1" <-> "NH2" Residue "2 ARG 74": "NH1" <-> "NH2" Residue "3 ARG 61": "NH1" <-> "NH2" Residue "3 ARG 102": "NH1" <-> "NH2" Residue "4 ARG 74": "NH1" <-> "NH2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ARG 27": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 160": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q ARG 102": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "T ARG 74": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "U ARG 61": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "V ARG 74": "NH1" <-> "NH2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W ARG 102": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49848 Number of models: 1 Model: "" Number of chains: 32 Chain: "5" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "6" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "7" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "8" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "O" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "P" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "G" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "2" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "3" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "4" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "N" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "E" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "J" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "Q" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "R" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "L" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "U" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "V" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "W" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "X" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 24.40, per 1000 atoms: 0.49 Number of scatterers: 49848 At special positions: 0 Unit cell: (202, 202, 133.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 9264 8.00 N 8824 7.00 C 31592 6.00 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: 18.02 Conformation dependent library (CDL) restraints added in 9.5 seconds 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11760 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 32 sheets defined 55.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain '5' and resid 4 through 30 removed outlier: 3.677A pdb=" N SER 5 16 " --> pdb=" O LYS 5 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN 5 29 " --> pdb=" O THR 5 25 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 38 Processing helix chain '5' and resid 53 through 60 Processing helix chain '5' and resid 65 through 79 removed outlier: 3.836A pdb=" N ARG 5 69 " --> pdb=" O ASP 5 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 5 74 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU 5 75 " --> pdb=" O MET 5 71 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HIS 5 76 " --> pdb=" O THR 5 72 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE 5 77 " --> pdb=" O VAL 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 102 removed outlier: 3.585A pdb=" N ARG 5 90 " --> pdb=" O PRO 5 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY 5 92 " --> pdb=" O MET 5 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN 5 94 " --> pdb=" O ARG 5 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN 5 95 " --> pdb=" O SER 5 91 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN 5 100 " --> pdb=" O ALA 5 96 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 31 removed outlier: 3.514A pdb=" N ASP 6 9 " --> pdb=" O GLN 6 5 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS 6 12 " --> pdb=" O LYS 6 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 6 14 " --> pdb=" O THR 6 10 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 34 through 46 removed outlier: 3.547A pdb=" N THR 6 43 " --> pdb=" O LEU 6 39 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 63 removed outlier: 3.821A pdb=" N LYS 6 57 " --> pdb=" O GLU 6 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU 6 58 " --> pdb=" O ALA 6 54 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU 6 62 " --> pdb=" O GLU 6 58 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 77 removed outlier: 3.809A pdb=" N ARG 6 69 " --> pdb=" O ASP 6 65 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL 6 73 " --> pdb=" O ARG 6 69 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG 6 74 " --> pdb=" O ILE 6 70 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU 6 75 " --> pdb=" O MET 6 71 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS 6 76 " --> pdb=" O THR 6 72 " (cutoff:3.500A) Processing helix chain '6' and resid 85 through 100 removed outlier: 4.159A pdb=" N ARG 6 90 " --> pdb=" O PRO 6 86 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER 6 91 " --> pdb=" O GLU 6 87 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 6 92 " --> pdb=" O MET 6 88 " (cutoff:3.500A) Processing helix chain '6' and resid 101 through 112 removed outlier: 3.795A pdb=" N LEU 6 105 " --> pdb=" O ARG 6 101 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 30 removed outlier: 3.530A pdb=" N THR 7 13 " --> pdb=" O ASP 7 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 7 16 " --> pdb=" O LYS 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 34 through 38 Processing helix chain '7' and resid 53 through 60 Processing helix chain '7' and resid 65 through 79 removed outlier: 3.807A pdb=" N ARG 7 69 " --> pdb=" O ASP 7 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG 7 74 " --> pdb=" O ILE 7 70 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU 7 75 " --> pdb=" O MET 7 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS 7 76 " --> pdb=" O THR 7 72 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 7 77 " --> pdb=" O VAL 7 73 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 102 removed outlier: 3.527A pdb=" N MET 7 88 " --> pdb=" O PHE 7 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 90 " --> pdb=" O PRO 7 86 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY 7 92 " --> pdb=" O MET 7 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN 7 94 " --> pdb=" O ARG 7 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN 7 95 " --> pdb=" O SER 7 91 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN 7 100 " --> pdb=" O ALA 7 96 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 31 removed outlier: 3.505A pdb=" N ASP 8 9 " --> pdb=" O GLN 8 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS 8 12 " --> pdb=" O LYS 8 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 8 14 " --> pdb=" O THR 8 10 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 46 removed outlier: 3.558A pdb=" N THR 8 43 " --> pdb=" O LEU 8 39 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL 8 46 " --> pdb=" O HIS 8 42 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 63 removed outlier: 3.834A pdb=" N LYS 8 57 " --> pdb=" O GLU 8 53 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU 8 58 " --> pdb=" O ALA 8 54 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU 8 62 " --> pdb=" O GLU 8 58 " (cutoff:3.500A) Processing helix chain '8' and resid 65 through 77 removed outlier: 3.788A pdb=" N ARG 8 69 " --> pdb=" O ASP 8 65 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL 8 73 " --> pdb=" O ARG 8 69 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG 8 74 " --> pdb=" O ILE 8 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU 8 75 " --> pdb=" O MET 8 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS 8 76 " --> pdb=" O THR 8 72 " (cutoff:3.500A) Processing helix chain '8' and resid 85 through 100 removed outlier: 4.148A pdb=" N ARG 8 90 " --> pdb=" O PRO 8 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER 8 91 " --> pdb=" O GLU 8 87 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY 8 92 " --> pdb=" O MET 8 88 " (cutoff:3.500A) Processing helix chain '8' and resid 101 through 112 removed outlier: 3.866A pdb=" N LEU 8 105 " --> pdb=" O ARG 8 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS O 25 " --> pdb=" O GLU O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU O 43 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 56 removed outlier: 3.597A pdb=" N ALA O 56 " --> pdb=" O ILE O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL O 67 " --> pdb=" O GLN O 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER O 76 " --> pdb=" O GLN O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU O 98 " --> pdb=" O GLY O 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR O 99 " --> pdb=" O SER O 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU O 101 " --> pdb=" O VAL O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 104 No H-bonds generated for 'chain 'O' and resid 102 through 104' Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 115 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE O 117 " --> pdb=" O GLY O 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU O 128 " --> pdb=" O ASP O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA O 155 " --> pdb=" O GLY O 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG O 171 " --> pdb=" O ASP O 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER O 172 " --> pdb=" O LEU O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 172' Processing helix chain 'O' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG O 177 " --> pdb=" O ARG O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE O 181 " --> pdb=" O ARG O 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA O 182 " --> pdb=" O GLY O 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 177 through 182' Processing helix chain 'O' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE O 191 " --> pdb=" O ALA O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS P 25 " --> pdb=" O GLU P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 44 removed outlier: 4.731A pdb=" N ALA P 41 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA P 56 " --> pdb=" O ILE P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 78 removed outlier: 3.829A pdb=" N GLN P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL P 69 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU P 98 " --> pdb=" O GLY P 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR P 99 " --> pdb=" O SER P 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU P 101 " --> pdb=" O VAL P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 104 No H-bonds generated for 'chain 'P' and resid 102 through 104' Processing helix chain 'P' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE P 117 " --> pdb=" O GLY P 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS P 119 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU P 128 " --> pdb=" O ASP P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA P 155 " --> pdb=" O GLY P 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP P 159 " --> pdb=" O ALA P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG P 171 " --> pdb=" O ASP P 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER P 172 " --> pdb=" O LEU P 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 167 through 172' Processing helix chain 'P' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG P 177 " --> pdb=" O ARG P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 182 removed outlier: 3.616A pdb=" N PHE P 181 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA P 182 " --> pdb=" O GLY P 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 177 through 182' Processing helix chain 'P' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE P 191 " --> pdb=" O ALA P 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP G 161 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA G 189 " --> pdb=" O ASN G 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 190 " --> pdb=" O TYR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG G 195 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY G 197 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 removed outlier: 3.606A pdb=" N PHE G 219 " --> pdb=" O TRP G 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 215 through 220' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 280 removed outlier: 3.538A pdb=" N THR G 279 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR G 280 " --> pdb=" O ALA G 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 276 through 280' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE G 346 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL G 347 " --> pdb=" O THR G 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 342 through 347' Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY G 362 " --> pdb=" O LYS G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL G 392 " --> pdb=" O MET G 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU G 393 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 422 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 423 " --> pdb=" O THR G 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL G 429 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN G 430 " --> pdb=" O GLU G 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL G 445 " --> pdb=" O GLU G 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL G 458 " --> pdb=" O PRO G 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 459 " --> pdb=" O GLU G 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 462 " --> pdb=" O VAL G 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 121 removed outlier: 3.912A pdb=" N VAL H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS H 147 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP H 161 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.616A pdb=" N ALA H 189 " --> pdb=" O ASN H 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL H 190 " --> pdb=" O TYR H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG H 195 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 197 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE H 219 " --> pdb=" O TRP H 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 220' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR H 279 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR H 280 " --> pdb=" O ALA H 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 276 through 280' Processing helix chain 'H' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE H 346 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL H 347 " --> pdb=" O THR H 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 342 through 347' Processing helix chain 'H' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY H 362 " --> pdb=" O LYS H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 396 removed outlier: 3.541A pdb=" N VAL H 392 " --> pdb=" O MET H 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 393 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG H 422 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 423 " --> pdb=" O THR H 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS H 428 " --> pdb=" O ALA H 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL H 429 " --> pdb=" O LEU H 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN H 430 " --> pdb=" O GLU H 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 431 " --> pdb=" O ALA H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 449 " --> pdb=" O VAL H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL H 458 " --> pdb=" O PRO H 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 30 removed outlier: 3.636A pdb=" N SER 1 16 " --> pdb=" O LYS 1 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN 1 29 " --> pdb=" O THR 1 25 " (cutoff:3.500A) Processing helix chain '1' and resid 34 through 38 Processing helix chain '1' and resid 53 through 60 Processing helix chain '1' and resid 65 through 79 removed outlier: 3.826A pdb=" N ARG 1 69 " --> pdb=" O ASP 1 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR 1 72 " --> pdb=" O LEU 1 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 1 74 " --> pdb=" O ILE 1 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU 1 75 " --> pdb=" O MET 1 71 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS 1 76 " --> pdb=" O THR 1 72 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE 1 77 " --> pdb=" O VAL 1 73 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 102 removed outlier: 3.765A pdb=" N ARG 1 90 " --> pdb=" O PRO 1 86 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY 1 92 " --> pdb=" O MET 1 88 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 1 94 " --> pdb=" O ARG 1 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 1 95 " --> pdb=" O SER 1 91 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN 1 100 " --> pdb=" O ALA 1 96 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 34 removed outlier: 3.506A pdb=" N ASP 2 9 " --> pdb=" O GLN 2 5 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS 2 12 " --> pdb=" O LYS 2 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 2 14 " --> pdb=" O THR 2 10 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU 2 32 " --> pdb=" O ALA 2 28 " (cutoff:3.500A) Processing helix chain '2' and resid 34 through 46 removed outlier: 3.505A pdb=" N THR 2 43 " --> pdb=" O LEU 2 39 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL 2 46 " --> pdb=" O HIS 2 42 " (cutoff:3.500A) Processing helix chain '2' and resid 51 through 63 removed outlier: 3.796A pdb=" N LYS 2 57 " --> pdb=" O GLU 2 53 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU 2 58 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG 2 61 " --> pdb=" O LYS 2 57 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 2 62 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 removed outlier: 3.821A pdb=" N ARG 2 69 " --> pdb=" O ASP 2 65 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL 2 73 " --> pdb=" O ARG 2 69 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG 2 74 " --> pdb=" O ILE 2 70 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU 2 75 " --> pdb=" O MET 2 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS 2 76 " --> pdb=" O THR 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 100 removed outlier: 4.170A pdb=" N ARG 2 90 " --> pdb=" O PRO 2 86 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER 2 91 " --> pdb=" O GLU 2 87 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY 2 92 " --> pdb=" O MET 2 88 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 112 removed outlier: 3.823A pdb=" N LEU 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 30 removed outlier: 3.656A pdb=" N SER 3 16 " --> pdb=" O LYS 3 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN 3 29 " --> pdb=" O THR 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 34 through 38 Processing helix chain '3' and resid 53 through 60 Processing helix chain '3' and resid 65 through 79 removed outlier: 3.830A pdb=" N ARG 3 69 " --> pdb=" O ASP 3 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR 3 72 " --> pdb=" O LEU 3 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 3 74 " --> pdb=" O ILE 3 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU 3 75 " --> pdb=" O MET 3 71 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS 3 76 " --> pdb=" O THR 3 72 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE 3 77 " --> pdb=" O VAL 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 102 removed outlier: 3.676A pdb=" N ARG 3 90 " --> pdb=" O PRO 3 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY 3 92 " --> pdb=" O MET 3 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN 3 94 " --> pdb=" O ARG 3 90 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN 3 95 " --> pdb=" O SER 3 91 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN 3 100 " --> pdb=" O ALA 3 96 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 34 removed outlier: 3.547A pdb=" N ASP 4 9 " --> pdb=" O GLN 4 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU 4 32 " --> pdb=" O ALA 4 28 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 46 removed outlier: 3.534A pdb=" N THR 4 43 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL 4 46 " --> pdb=" O HIS 4 42 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 63 removed outlier: 3.796A pdb=" N LYS 4 57 " --> pdb=" O GLU 4 53 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU 4 58 " --> pdb=" O ALA 4 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG 4 61 " --> pdb=" O LYS 4 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU 4 62 " --> pdb=" O GLU 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 65 through 77 removed outlier: 3.823A pdb=" N ARG 4 69 " --> pdb=" O ASP 4 65 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL 4 73 " --> pdb=" O ARG 4 69 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG 4 74 " --> pdb=" O ILE 4 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU 4 75 " --> pdb=" O MET 4 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS 4 76 " --> pdb=" O THR 4 72 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 100 removed outlier: 4.173A pdb=" N ARG 4 90 " --> pdb=" O PRO 4 86 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER 4 91 " --> pdb=" O GLU 4 87 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY 4 92 " --> pdb=" O MET 4 88 " (cutoff:3.500A) Processing helix chain '4' and resid 101 through 112 removed outlier: 3.851A pdb=" N LEU 4 105 " --> pdb=" O ARG 4 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 25 removed outlier: 3.741A pdb=" N LYS M 25 " --> pdb=" O GLU M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M 43 " --> pdb=" O ALA M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA M 56 " --> pdb=" O ILE M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 78 removed outlier: 3.829A pdb=" N GLN M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL M 67 " --> pdb=" O GLN M 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR M 99 " --> pdb=" O SER M 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 101 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 104 No H-bonds generated for 'chain 'M' and resid 102 through 104' Processing helix chain 'M' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP M 114 " --> pdb=" O ALA M 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE M 117 " --> pdb=" O GLY M 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU M 128 " --> pdb=" O ASP M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA M 155 " --> pdb=" O GLY M 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG M 171 " --> pdb=" O ASP M 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 167 through 172' Processing helix chain 'M' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG M 177 " --> pdb=" O ARG M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE M 181 " --> pdb=" O ARG M 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 177 through 182' Processing helix chain 'M' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE M 191 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS N 25 " --> pdb=" O GLU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA N 56 " --> pdb=" O ILE N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN N 66 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL N 67 " --> pdb=" O GLN N 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL N 69 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER N 76 " --> pdb=" O GLN N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU N 98 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 104 No H-bonds generated for 'chain 'N' and resid 102 through 104' Processing helix chain 'N' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE N 117 " --> pdb=" O GLY N 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU N 128 " --> pdb=" O ASP N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA N 155 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP N 159 " --> pdb=" O ALA N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG N 171 " --> pdb=" O ASP N 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 167 through 172' Processing helix chain 'N' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG N 177 " --> pdb=" O ARG N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE N 181 " --> pdb=" O ARG N 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA N 182 " --> pdb=" O GLY N 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 177 through 182' Processing helix chain 'N' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP E 161 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 190 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG E 195 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE E 219 " --> pdb=" O TRP E 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 220' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.540A pdb=" N THR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 280 " --> pdb=" O ALA E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 276 through 280' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.614A pdb=" N LEU E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE E 346 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 347' Processing helix chain 'E' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY E 362 " --> pdb=" O LYS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL E 392 " --> pdb=" O MET E 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 423 " --> pdb=" O THR E 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL E 458 " --> pdb=" O PRO E 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.914A pdb=" N VAL F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS F 147 " --> pdb=" O VAL F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP F 161 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL F 190 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG F 195 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE F 219 " --> pdb=" O TRP F 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 215 through 220' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 280 " --> pdb=" O ALA F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 276 through 280' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE F 346 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 342 through 347' Processing helix chain 'F' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY F 362 " --> pdb=" O LYS F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL F 392 " --> pdb=" O MET F 388 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 423 " --> pdb=" O THR F 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN F 430 " --> pdb=" O GLU F 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 431 " --> pdb=" O ALA F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 removed outlier: 3.718A pdb=" N VAL F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 463 removed outlier: 3.752A pdb=" N VAL F 458 " --> pdb=" O PRO F 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS I 25 " --> pdb=" O GLU I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA I 56 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL I 67 " --> pdb=" O GLN I 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL I 69 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 4.206A pdb=" N ALA I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 108 through 119 removed outlier: 3.601A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA I 155 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG I 171 " --> pdb=" O ASP I 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 167 through 172' Processing helix chain 'I' and resid 172 through 177 removed outlier: 4.045A pdb=" N ARG I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE I 181 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA I 182 " --> pdb=" O GLY I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 182' Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS J 25 " --> pdb=" O GLU J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 44 removed outlier: 4.729A pdb=" N ALA J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.599A pdb=" N ALA J 56 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL J 67 " --> pdb=" O GLN J 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 69 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER J 76 " --> pdb=" O GLN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU J 98 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR J 99 " --> pdb=" O SER J 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 101 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 104 No H-bonds generated for 'chain 'J' and resid 102 through 104' Processing helix chain 'J' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA J 155 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 167 through 172' Processing helix chain 'J' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE J 181 " --> pdb=" O ARG J 177 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA J 182 " --> pdb=" O GLY J 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 182' Processing helix chain 'J' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 30 removed outlier: 3.617A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN Q 29 " --> pdb=" O THR Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 Processing helix chain 'Q' and resid 53 through 60 Processing helix chain 'Q' and resid 65 through 79 removed outlier: 3.851A pdb=" N ARG Q 69 " --> pdb=" O ASP Q 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG Q 74 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU Q 75 " --> pdb=" O MET Q 71 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS Q 76 " --> pdb=" O THR Q 72 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE Q 77 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 102 removed outlier: 3.554A pdb=" N MET Q 88 " --> pdb=" O PHE Q 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG Q 90 " --> pdb=" O PRO Q 86 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY Q 92 " --> pdb=" O MET Q 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN Q 94 " --> pdb=" O ARG Q 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN Q 95 " --> pdb=" O SER Q 91 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 31 removed outlier: 3.505A pdb=" N ASP R 9 " --> pdb=" O GLN R 5 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 14 " --> pdb=" O THR R 10 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.523A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL R 46 " --> pdb=" O HIS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 63 removed outlier: 3.880A pdb=" N LYS R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU R 58 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 removed outlier: 3.784A pdb=" N ARG R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 100 removed outlier: 4.144A pdb=" N ARG R 90 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER R 91 " --> pdb=" O GLU R 87 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY R 92 " --> pdb=" O MET R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 112 removed outlier: 3.815A pdb=" N LEU R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 30 removed outlier: 3.514A pdb=" N THR S 13 " --> pdb=" O ASP S 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 38 Processing helix chain 'S' and resid 53 through 60 Processing helix chain 'S' and resid 65 through 79 removed outlier: 3.825A pdb=" N ARG S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR S 72 " --> pdb=" O LEU S 68 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU S 75 " --> pdb=" O MET S 71 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS S 76 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE S 77 " --> pdb=" O VAL S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 102 removed outlier: 3.528A pdb=" N MET S 88 " --> pdb=" O PHE S 84 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG S 90 " --> pdb=" O PRO S 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY S 92 " --> pdb=" O MET S 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN S 95 " --> pdb=" O SER S 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 34 removed outlier: 3.508A pdb=" N ASP T 9 " --> pdb=" O GLN T 5 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 14 " --> pdb=" O THR T 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.520A pdb=" N THR T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 63 removed outlier: 3.808A pdb=" N LYS T 57 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU T 58 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU T 62 " --> pdb=" O GLU T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 77 removed outlier: 3.815A pdb=" N ARG T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG T 74 " --> pdb=" O ILE T 70 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU T 75 " --> pdb=" O MET T 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS T 76 " --> pdb=" O THR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 100 removed outlier: 4.138A pdb=" N ARG T 90 " --> pdb=" O PRO T 86 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY T 92 " --> pdb=" O MET T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 112 removed outlier: 3.799A pdb=" N LEU T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.914A pdb=" N VAL A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP A 161 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 220' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 280 " --> pdb=" O ALA A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.747A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 347' Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL A 392 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.752A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP B 161 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 220' Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 280 " --> pdb=" O ALA B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 276 through 280' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 347' Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL B 392 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 25 removed outlier: 3.743A pdb=" N LYS K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA K 56 " --> pdb=" O ILE K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN K 66 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL K 69 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU K 98 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU K 101 " --> pdb=" O VAL K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 104 No H-bonds generated for 'chain 'K' and resid 102 through 104' Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU K 128 " --> pdb=" O ASP K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA K 155 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP K 159 " --> pdb=" O ALA K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 172 removed outlier: 3.660A pdb=" N ARG K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 167 through 172' Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG K 177 " --> pdb=" O ARG K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE K 181 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA K 182 " --> pdb=" O GLY K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 177 through 182' Processing helix chain 'K' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS L 25 " --> pdb=" O GLU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 44 removed outlier: 4.729A pdb=" N ALA L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 56 removed outlier: 3.599A pdb=" N ALA L 56 " --> pdb=" O ILE L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN L 66 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL L 67 " --> pdb=" O GLN L 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 69 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU L 98 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 99 " --> pdb=" O SER L 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU L 101 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 104 No H-bonds generated for 'chain 'L' and resid 102 through 104' Processing helix chain 'L' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 117 " --> pdb=" O GLY L 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG L 171 " --> pdb=" O ASP L 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 167 through 172' Processing helix chain 'L' and resid 172 through 177 removed outlier: 4.045A pdb=" N ARG L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE L 181 " --> pdb=" O ARG L 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 177 through 182' Processing helix chain 'L' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 30 removed outlier: 3.665A pdb=" N SER U 16 " --> pdb=" O LYS U 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN U 29 " --> pdb=" O THR U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 38 Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 65 through 79 removed outlier: 3.847A pdb=" N ARG U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 72 " --> pdb=" O LEU U 68 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG U 74 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS U 76 " --> pdb=" O THR U 72 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE U 77 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 102 removed outlier: 3.752A pdb=" N ARG U 90 " --> pdb=" O PRO U 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY U 92 " --> pdb=" O MET U 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN U 94 " --> pdb=" O ARG U 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN U 95 " --> pdb=" O SER U 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN U 100 " --> pdb=" O ALA U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 34 removed outlier: 3.503A pdb=" N ASP V 9 " --> pdb=" O GLN V 5 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU V 14 " --> pdb=" O THR V 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN V 15 " --> pdb=" O ALA V 11 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU V 32 " --> pdb=" O ALA V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.505A pdb=" N THR V 43 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL V 46 " --> pdb=" O HIS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 63 removed outlier: 3.824A pdb=" N LYS V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU V 62 " --> pdb=" O GLU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 77 removed outlier: 3.820A pdb=" N ARG V 69 " --> pdb=" O ASP V 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET V 71 " --> pdb=" O ALA V 67 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL V 73 " --> pdb=" O ARG V 69 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG V 74 " --> pdb=" O ILE V 70 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU V 75 " --> pdb=" O MET V 71 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS V 76 " --> pdb=" O THR V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 100 removed outlier: 4.175A pdb=" N ARG V 90 " --> pdb=" O PRO V 86 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER V 91 " --> pdb=" O GLU V 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY V 92 " --> pdb=" O MET V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 112 removed outlier: 3.818A pdb=" N LEU V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 30 removed outlier: 3.527A pdb=" N THR W 13 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 38 Processing helix chain 'W' and resid 53 through 60 Processing helix chain 'W' and resid 65 through 79 removed outlier: 3.809A pdb=" N ARG W 69 " --> pdb=" O ASP W 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG W 74 " --> pdb=" O ILE W 70 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU W 75 " --> pdb=" O MET W 71 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS W 76 " --> pdb=" O THR W 72 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE W 77 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 102 removed outlier: 3.524A pdb=" N MET W 88 " --> pdb=" O PHE W 84 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG W 90 " --> pdb=" O PRO W 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY W 92 " --> pdb=" O MET W 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN W 94 " --> pdb=" O ARG W 90 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN W 95 " --> pdb=" O SER W 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN W 100 " --> pdb=" O ALA W 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 34 removed outlier: 3.507A pdb=" N ASP X 9 " --> pdb=" O GLN X 5 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS X 12 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR X 13 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU X 14 " --> pdb=" O THR X 10 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN X 15 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR X 20 " --> pdb=" O SER X 16 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 46 removed outlier: 3.502A pdb=" N THR X 43 " --> pdb=" O LEU X 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL X 46 " --> pdb=" O HIS X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 63 removed outlier: 3.839A pdb=" N LYS X 57 " --> pdb=" O GLU X 53 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 77 removed outlier: 3.800A pdb=" N ARG X 69 " --> pdb=" O ASP X 65 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL X 73 " --> pdb=" O ARG X 69 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG X 74 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU X 75 " --> pdb=" O MET X 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS X 76 " --> pdb=" O THR X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 100 removed outlier: 4.147A pdb=" N ARG X 90 " --> pdb=" O PRO X 86 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY X 92 " --> pdb=" O MET X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 removed outlier: 3.837A pdb=" N LEU X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 121 removed outlier: 3.912A pdb=" N VAL C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE C 219 " --> pdb=" O TRP C 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 220' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR C 279 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 280 " --> pdb=" O ALA C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 280' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE C 346 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 342 through 347' Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL C 392 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 removed outlier: 4.715A pdb=" N ASN C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 449 removed outlier: 3.718A pdb=" N VAL C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 446 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP D 161 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE D 219 " --> pdb=" O TRP D 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 220' Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR D 257 " --> pdb=" O LYS D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 280 " --> pdb=" O ALA D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 280' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.747A pdb=" N PHE D 346 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 342 through 347' Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 396 removed outlier: 3.541A pdb=" N VAL D 392 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 393 " --> pdb=" O PRO D 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG G 42 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 134 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR G 44 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 38 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS G 173 " --> pdb=" O LYS G 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE G 294 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG H 42 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 134 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 44 " --> pdb=" O ARG H 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 38 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS H 173 " --> pdb=" O LYS H 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE H 294 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA H 377 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG E 42 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 134 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR E 44 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 38 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 172 through 174 removed outlier: 6.833A pdb=" N CYS E 173 " --> pdb=" O LYS E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 293 through 294 removed outlier: 3.581A pdb=" N ILE E 294 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG F 42 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 134 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR F 44 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 38 " --> pdb=" O ARG F 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 172 through 174 removed outlier: 6.835A pdb=" N CYS F 173 " --> pdb=" O LYS F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE F 294 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA F 377 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 42 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 134 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 44 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 38 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS A 173 " --> pdb=" O LYS A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE A 294 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG B 42 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 134 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 44 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 38 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS B 173 " --> pdb=" O LYS B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE B 294 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA B 377 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG C 42 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 134 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 44 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 38 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS C 173 " --> pdb=" O LYS C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 293 through 294 removed outlier: 3.581A pdb=" N ILE C 294 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG D 42 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 134 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 44 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 38 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 172 through 174 removed outlier: 6.833A pdb=" N CYS D 173 " --> pdb=" O LYS D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE D 294 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA D 377 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1637 hydrogen bonds defined for protein. 4623 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: 17.78 Time building geometry restraints manager: 19.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15616 1.34 - 1.46: 9551 1.46 - 1.58: 25407 1.58 - 1.70: 2 1.70 - 1.82: 280 Bond restraints: 50856 Sorted by residual: bond pdb=" C LEU F 372 " pdb=" N PRO F 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" C LEU B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" C LEU E 372 " pdb=" N PRO E 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.80e+01 bond pdb=" C LEU A 372 " pdb=" N PRO A 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" C LEU G 372 " pdb=" N PRO G 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.78e+01 ... (remaining 50851 not shown) Histogram of bond angle deviations from ideal: 94.87 - 103.27: 520 103.27 - 111.67: 20832 111.67 - 120.07: 26117 120.07 - 128.47: 20877 128.47 - 136.88: 470 Bond angle restraints: 68816 Sorted by residual: angle pdb=" CA LEU D 291 " pdb=" CB LEU D 291 " pdb=" CG LEU D 291 " ideal model delta sigma weight residual 116.30 136.88 -20.58 3.50e+00 8.16e-02 3.46e+01 angle pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " pdb=" CG LEU B 291 " ideal model delta sigma weight residual 116.30 136.87 -20.57 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU G 291 " pdb=" CB LEU G 291 " pdb=" CG LEU G 291 " ideal model delta sigma weight residual 116.30 136.86 -20.56 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU A 291 " pdb=" CB LEU A 291 " pdb=" CG LEU A 291 " ideal model delta sigma weight residual 116.30 136.86 -20.56 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU H 291 " pdb=" CB LEU H 291 " pdb=" CG LEU H 291 " ideal model delta sigma weight residual 116.30 136.83 -20.53 3.50e+00 8.16e-02 3.44e+01 ... (remaining 68811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 28528 15.52 - 31.04: 1616 31.04 - 46.56: 312 46.56 - 62.08: 40 62.08 - 77.60: 48 Dihedral angle restraints: 30544 sinusoidal: 12360 harmonic: 18184 Sorted by residual: dihedral pdb=" CA GLU E 260 " pdb=" C GLU E 260 " pdb=" N LEU E 261 " pdb=" CA LEU E 261 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA GLU F 260 " pdb=" C GLU F 260 " pdb=" N LEU F 261 " pdb=" CA LEU F 261 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA GLU H 260 " pdb=" C GLU H 260 " pdb=" N LEU H 261 " pdb=" CA LEU H 261 " ideal model delta harmonic sigma weight residual 180.00 140.50 39.50 0 5.00e+00 4.00e-02 6.24e+01 ... (remaining 30541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 6573 0.089 - 0.177: 928 0.177 - 0.266: 43 0.266 - 0.355: 22 0.355 - 0.444: 10 Chirality restraints: 7576 Sorted by residual: chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CB VAL F 222 " pdb=" CA VAL F 222 " pdb=" CG1 VAL F 222 " pdb=" CG2 VAL F 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB VAL A 222 " pdb=" CA VAL A 222 " pdb=" CG1 VAL A 222 " pdb=" CG2 VAL A 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 7573 not shown) Planarity restraints: 8976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO W 35 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO W 36 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO W 36 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO W 36 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO S 35 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO S 36 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO S 36 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 36 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO 7 35 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO 7 36 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO 7 36 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO 7 36 " -0.043 5.00e-02 4.00e+02 ... (remaining 8973 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11540 2.78 - 3.31: 43024 3.31 - 3.84: 78113 3.84 - 4.37: 96176 4.37 - 4.90: 155018 Nonbonded interactions: 383871 Sorted by model distance: nonbonded pdb=" O PHE G 275 " pdb=" OG1 THR G 279 " model vdw 2.253 2.440 nonbonded pdb=" O PHE H 275 " pdb=" OG1 THR H 279 " model vdw 2.254 2.440 nonbonded pdb=" O PHE B 275 " pdb=" OG1 THR B 279 " model vdw 2.254 2.440 nonbonded pdb=" O PHE F 275 " pdb=" OG1 THR F 279 " model vdw 2.254 2.440 nonbonded pdb=" O PHE D 275 " pdb=" OG1 THR D 279 " model vdw 2.254 2.440 ... (remaining 383866 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 '1' selection = (chain '2' and resid 2 through 102) selection = chain '3' selection = (chain '4' and resid 2 through 102) selection = chain '5' selection = (chain '6' and resid 2 through 102) selection = chain '7' selection = (chain '8' and resid 2 through 102) selection = chain 'Q' selection = (chain 'R' and resid 2 through 102) selection = chain 'S' selection = (chain 'T' and resid 2 through 102) selection = chain 'U' selection = (chain 'V' and resid 2 through 102) selection = chain 'W' selection = (chain 'X' and resid 2 through 102) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.620 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: 0.040 Extract box with map and model: 7.660 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 119.920 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.370 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 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 : 0.009 0.095 50856 Z= 0.572 Angle : 1.336 20.576 68816 Z= 0.733 Chirality : 0.063 0.444 7576 Planarity : 0.009 0.077 8976 Dihedral : 11.072 77.603 18784 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 0.77 % Allowed : 2.88 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.61 (0.08), residues: 6128 helix: -4.39 (0.05), residues: 3032 sheet: -4.31 (0.19), residues: 288 loop : -2.70 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP H 284 HIS 0.016 0.003 HIS E 326 PHE 0.044 0.006 PHE F 219 TYR 0.029 0.004 TYR L 48 ARG 0.020 0.002 ARG W 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1579 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 26 VAL cc_start: 0.6945 (t) cc_final: 0.6464 (t) REVERT: 5 44 PHE cc_start: 0.3105 (m-80) cc_final: 0.2478 (m-80) REVERT: 5 68 LEU cc_start: 0.4453 (mt) cc_final: 0.4206 (tp) REVERT: 5 98 MET cc_start: 0.5861 (mmm) cc_final: 0.5259 (mmm) REVERT: 6 13 THR cc_start: 0.4466 (m) cc_final: 0.3683 (p) REVERT: 6 94 GLN cc_start: 0.6359 (mt0) cc_final: 0.5988 (mm110) REVERT: 7 24 MET cc_start: 0.5431 (mmm) cc_final: 0.5152 (tpp) REVERT: 7 25 THR cc_start: 0.5791 (m) cc_final: 0.5563 (m) REVERT: 7 66 LEU cc_start: 0.6407 (mt) cc_final: 0.6152 (tp) REVERT: 7 71 MET cc_start: 0.3875 (mmt) cc_final: 0.3544 (mmt) REVERT: 7 81 VAL cc_start: 0.5706 (t) cc_final: 0.5177 (p) REVERT: 8 3 LEU cc_start: 0.5881 (tp) cc_final: 0.5550 (mt) REVERT: 8 100 GLN cc_start: 0.2575 (mt0) cc_final: 0.1985 (mp10) REVERT: 8 104 HIS cc_start: 0.3313 (t70) cc_final: 0.3046 (m-70) REVERT: O 33 TRP cc_start: 0.5667 (p-90) cc_final: 0.5051 (p-90) REVERT: H 53 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5784 (mm-30) REVERT: 1 18 LEU cc_start: 0.6077 (mt) cc_final: 0.5773 (tt) REVERT: 1 24 MET cc_start: 0.6327 (mmm) cc_final: 0.6015 (ppp) REVERT: 1 26 VAL cc_start: 0.5373 (t) cc_final: 0.4888 (t) REVERT: 2 13 THR cc_start: 0.3526 (m) cc_final: 0.3154 (p) REVERT: 2 105 LEU cc_start: 0.4948 (mm) cc_final: 0.4216 (tp) REVERT: 2 108 MET cc_start: 0.5098 (tpp) cc_final: 0.4352 (ptm) REVERT: 3 97 ASN cc_start: 0.2820 (m-40) cc_final: 0.2494 (t0) REVERT: 4 76 HIS cc_start: 0.5363 (t70) cc_final: 0.5006 (t-90) REVERT: M 26 LEU cc_start: 0.5466 (tt) cc_final: 0.4768 (tt) REVERT: F 327 ILE cc_start: 0.6556 (pt) cc_final: 0.6267 (pt) REVERT: I 27 ARG cc_start: 0.4382 (ptm-80) cc_final: 0.3196 (mtm180) REVERT: Q 68 LEU cc_start: 0.4922 (mt) cc_final: 0.4274 (tp) REVERT: R 95 GLN cc_start: 0.5976 (mt0) cc_final: 0.5758 (mm110) REVERT: S 20 TYR cc_start: 0.5598 (t80) cc_final: 0.5114 (t80) REVERT: S 21 GLN cc_start: 0.5219 (mm110) cc_final: 0.4362 (mm-40) REVERT: S 74 ARG cc_start: 0.3347 (ptt180) cc_final: 0.2983 (ttp-110) REVERT: S 86 PRO cc_start: 0.3700 (Cg_exo) cc_final: 0.3262 (Cg_endo) REVERT: A 421 ASN cc_start: 0.6689 (m-40) cc_final: 0.5976 (t0) REVERT: A 467 LYS cc_start: 0.6455 (mttt) cc_final: 0.5857 (mptt) REVERT: B 387 HIS cc_start: 0.2366 (m-70) cc_final: 0.2051 (m-70) REVERT: K 26 LEU cc_start: 0.4865 (tt) cc_final: 0.4401 (tt) REVERT: K 27 ARG cc_start: 0.4025 (ptm-80) cc_final: 0.3678 (mtm180) REVERT: K 118 THR cc_start: 0.6822 (m) cc_final: 0.6547 (p) REVERT: K 124 ASP cc_start: 0.7242 (m-30) cc_final: 0.6566 (m-30) REVERT: K 135 ASP cc_start: 0.5492 (m-30) cc_final: 0.5047 (m-30) REVERT: L 192 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5275 (mm-30) REVERT: U 4 LYS cc_start: 0.4300 (mtpm) cc_final: 0.3943 (mtpp) REVERT: U 24 MET cc_start: 0.6044 (mmm) cc_final: 0.5836 (tpp) REVERT: U 48 LYS cc_start: 0.4151 (mttt) cc_final: 0.3918 (tppt) REVERT: U 68 LEU cc_start: 0.3517 (mt) cc_final: 0.2983 (tp) REVERT: U 102 ARG cc_start: 0.4329 (ptm-80) cc_final: 0.3952 (ptm-80) REVERT: V 108 MET cc_start: 0.4756 (tpp) cc_final: 0.4474 (ptt) REVERT: W 24 MET cc_start: 0.5917 (mmm) cc_final: 0.5577 (ppp) REVERT: W 66 LEU cc_start: 0.6517 (mt) cc_final: 0.6314 (mp) REVERT: X 100 GLN cc_start: 0.3792 (mt0) cc_final: 0.3512 (mt0) REVERT: X 108 MET cc_start: 0.5451 (tpp) cc_final: 0.4969 (ptt) REVERT: C 215 TRP cc_start: 0.5067 (p-90) cc_final: 0.3868 (p-90) outliers start: 40 outliers final: 7 residues processed: 1598 average time/residue: 0.7122 time to fit residues: 1798.3906 Evaluate side-chains 830 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 823 time to evaluate : 5.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain D residue 267 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 482 optimal weight: 0.2980 chunk 186 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 359 optimal weight: 6.9990 chunk 559 optimal weight: 0.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 15 GLN 5 21 GLN 5 34 ASN 7 15 GLN 7 21 GLN 7 34 ASN 7 76 HIS 8 21 GLN O 30 GLN O 64 GLN O 65 ASN O 66 GLN P 30 GLN P 64 GLN P 66 GLN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 HIS G 308 HIS ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 HIS H 164 ASN H 206 ASN H 242 ASN ** H 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 ASN 1 15 GLN 1 21 GLN 1 34 ASN 2 21 GLN 2 29 GLN 2 97 ASN 3 15 GLN 3 21 GLN 3 34 ASN 4 21 GLN 4 29 GLN M 30 GLN M 64 GLN M 65 ASN M 66 GLN N 30 GLN E 116 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 206 ASN E 208 ASN E 242 ASN ** E 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS E 353 ASN F 164 ASN F 206 ASN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS F 311 HIS I 30 GLN I 64 GLN I 65 ASN I 66 GLN J 30 GLN J 44 GLN J 64 GLN J 65 ASN J 66 GLN ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 GLN Q 34 ASN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN S 15 GLN S 21 GLN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 206 ASN A 242 ASN A 308 HIS A 311 HIS A 353 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS B 443 ASN K 30 GLN K 64 GLN K 65 ASN K 66 GLN L 30 GLN L 65 ASN L 66 GLN U 21 GLN U 34 ASN U 76 HIS U 100 GLN V 15 GLN V 29 GLN W 15 GLN W 21 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 21 GLN X 29 GLN X 103 GLN C 124 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 206 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 206 ASN D 208 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 308 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 50856 Z= 0.262 Angle : 0.749 13.444 68816 Z= 0.388 Chirality : 0.045 0.232 7576 Planarity : 0.006 0.076 8976 Dihedral : 6.373 37.903 6859 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.52 % Allowed : 11.09 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.43 (0.09), residues: 6128 helix: -3.12 (0.07), residues: 3280 sheet: -3.61 (0.19), residues: 400 loop : -2.26 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP K 36 HIS 0.008 0.002 HIS B 293 PHE 0.024 0.002 PHE V 60 TYR 0.031 0.002 TYR S 20 ARG 0.007 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1046 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 88 MET cc_start: 0.2378 (tpp) cc_final: 0.2013 (mmm) REVERT: 5 98 MET cc_start: 0.5495 (mmm) cc_final: 0.4923 (mmm) REVERT: 6 94 GLN cc_start: 0.6484 (mt0) cc_final: 0.6099 (mm110) REVERT: 7 16 SER cc_start: 0.1635 (m) cc_final: 0.1372 (p) REVERT: 7 24 MET cc_start: 0.5446 (mmm) cc_final: 0.5135 (tpp) REVERT: 8 85 LEU cc_start: 0.3912 (mt) cc_final: 0.3711 (mt) REVERT: 8 98 MET cc_start: 0.6823 (tpp) cc_final: 0.6092 (mmt) REVERT: O 24 ARG cc_start: 0.5562 (ttp80) cc_final: 0.4879 (tpt90) REVERT: O 32 ASN cc_start: 0.6817 (p0) cc_final: 0.6606 (p0) REVERT: O 48 TYR cc_start: 0.5451 (OUTLIER) cc_final: 0.4865 (m-10) REVERT: O 120 LYS cc_start: 0.7153 (tptt) cc_final: 0.6642 (mptt) REVERT: O 193 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4774 (tm-30) REVERT: P 128 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5212 (mp0) REVERT: H 387 HIS cc_start: 0.2183 (m-70) cc_final: 0.1528 (m-70) REVERT: 1 3 LEU cc_start: 0.3593 (mt) cc_final: 0.2694 (tp) REVERT: 1 20 TYR cc_start: 0.5802 (t80) cc_final: 0.5113 (t80) REVERT: 1 24 MET cc_start: 0.6398 (mmm) cc_final: 0.5351 (mtp) REVERT: 2 13 THR cc_start: 0.3194 (m) cc_final: 0.2911 (p) REVERT: 2 83 GLU cc_start: 0.4317 (tp30) cc_final: 0.3594 (tm-30) REVERT: 2 98 MET cc_start: 0.6908 (mpp) cc_final: 0.6328 (mpp) REVERT: 2 105 LEU cc_start: 0.4608 (mm) cc_final: 0.4203 (tp) REVERT: 2 108 MET cc_start: 0.5562 (tpp) cc_final: 0.4699 (ptm) REVERT: 4 76 HIS cc_start: 0.5048 (t70) cc_final: 0.4648 (t70) REVERT: 4 108 MET cc_start: 0.3816 (mmt) cc_final: 0.3279 (mmm) REVERT: M 26 LEU cc_start: 0.5754 (tt) cc_final: 0.5461 (tt) REVERT: M 120 LYS cc_start: 0.7409 (tptp) cc_final: 0.7107 (mptt) REVERT: M 179 LEU cc_start: 0.7830 (mt) cc_final: 0.7441 (mp) REVERT: M 188 ARG cc_start: 0.5883 (tpp80) cc_final: 0.5554 (tpp-160) REVERT: N 129 ILE cc_start: 0.6317 (mm) cc_final: 0.6024 (tt) REVERT: N 140 ARG cc_start: 0.6114 (mpt180) cc_final: 0.5288 (ptt90) REVERT: E 211 PRO cc_start: 0.7300 (Cg_endo) cc_final: 0.7057 (Cg_exo) REVERT: E 270 TYR cc_start: 0.5983 (p90) cc_final: 0.5599 (p90) REVERT: E 426 GLU cc_start: 0.5457 (pt0) cc_final: 0.4769 (mt-10) REVERT: F 281 LEU cc_start: 0.6007 (mt) cc_final: 0.5804 (mp) REVERT: F 365 PHE cc_start: 0.6729 (m-80) cc_final: 0.6496 (m-80) REVERT: I 27 ARG cc_start: 0.4779 (ptm-80) cc_final: 0.3569 (mtp180) REVERT: Q 80 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6702 (mt-10) REVERT: R 24 MET cc_start: 0.1219 (mmm) cc_final: 0.0476 (tpt) REVERT: S 13 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.5565 (t) REVERT: S 16 SER cc_start: 0.3660 (m) cc_final: 0.2986 (p) REVERT: S 24 MET cc_start: 0.6132 (ptp) cc_final: 0.5723 (mmm) REVERT: S 74 ARG cc_start: 0.4034 (ptt180) cc_final: 0.3628 (ttp-110) REVERT: A 421 ASN cc_start: 0.6472 (m-40) cc_final: 0.6084 (t0) REVERT: B 161 ASP cc_start: 0.5389 (t0) cc_final: 0.5134 (t70) REVERT: B 443 ASN cc_start: 0.6358 (OUTLIER) cc_final: 0.6103 (m-40) REVERT: K 26 LEU cc_start: 0.5187 (tt) cc_final: 0.4665 (tt) REVERT: K 27 ARG cc_start: 0.4232 (ptm-80) cc_final: 0.3601 (mtt180) REVERT: K 55 GLU cc_start: 0.5456 (tt0) cc_final: 0.4839 (mm-30) REVERT: K 124 ASP cc_start: 0.6391 (m-30) cc_final: 0.6031 (m-30) REVERT: U 68 LEU cc_start: 0.3339 (mt) cc_final: 0.3016 (tp) REVERT: V 83 GLU cc_start: 0.4623 (mm-30) cc_final: 0.3555 (mp0) REVERT: V 84 PHE cc_start: 0.5927 (m-10) cc_final: 0.5542 (t80) REVERT: W 24 MET cc_start: 0.6265 (mmm) cc_final: 0.5725 (ppp) REVERT: W 68 LEU cc_start: 0.4420 (pp) cc_final: 0.4218 (pp) REVERT: X 107 ARG cc_start: 0.6314 (mpt180) cc_final: 0.5762 (ptt-90) REVERT: X 108 MET cc_start: 0.5593 (tpp) cc_final: 0.5134 (ptt) REVERT: C 270 TYR cc_start: 0.4770 (p90) cc_final: 0.4481 (p90) outliers start: 182 outliers final: 102 residues processed: 1166 average time/residue: 0.6206 time to fit residues: 1183.1467 Evaluate side-chains 888 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 781 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 465 optimal weight: 8.9990 chunk 380 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 560 optimal weight: 1.9990 chunk 605 optimal weight: 10.0000 chunk 499 optimal weight: 1.9990 chunk 555 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 449 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 97 ASN ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 HIS ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS G 387 HIS ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 357 GLN H 387 HIS 2 97 ASN 3 15 GLN ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 421 ASN F 116 ASN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN J 64 GLN J 66 GLN ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 387 HIS K 66 GLN K 193 GLN L 30 GLN L 65 ASN L 66 GLN L 106 HIS U 76 HIS ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 50856 Z= 0.301 Angle : 0.756 14.083 68816 Z= 0.394 Chirality : 0.045 0.246 7576 Planarity : 0.006 0.064 8976 Dihedral : 6.342 35.298 6858 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.14 % Allowed : 13.93 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.74 (0.09), residues: 6128 helix: -2.48 (0.08), residues: 3248 sheet: -3.39 (0.22), residues: 360 loop : -2.12 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP K 36 HIS 0.031 0.002 HIS F 268 PHE 0.034 0.003 PHE 7 44 TYR 0.023 0.002 TYR K 156 ARG 0.009 0.001 ARG W 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 941 time to evaluate : 5.838 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: 5 88 MET cc_start: 0.2137 (tpp) cc_final: 0.1853 (mmm) REVERT: 5 93 ILE cc_start: 0.3878 (mt) cc_final: 0.3387 (tp) REVERT: 5 98 MET cc_start: 0.5453 (mmm) cc_final: 0.4882 (mmm) REVERT: 6 94 GLN cc_start: 0.6462 (mt0) cc_final: 0.6119 (mm110) REVERT: 6 98 MET cc_start: 0.6291 (mmt) cc_final: 0.5984 (mmt) REVERT: 6 102 ARG cc_start: 0.4774 (mmt180) cc_final: 0.4415 (mmt180) REVERT: 7 16 SER cc_start: 0.2220 (m) cc_final: 0.1935 (p) REVERT: 7 24 MET cc_start: 0.5998 (mmm) cc_final: 0.5483 (tpp) REVERT: 7 66 LEU cc_start: 0.6508 (tp) cc_final: 0.6298 (tt) REVERT: 7 80 GLU cc_start: 0.5425 (mm-30) cc_final: 0.4906 (mt-10) REVERT: 8 98 MET cc_start: 0.6902 (tpp) cc_final: 0.6210 (mmt) REVERT: O 20 GLN cc_start: 0.5000 (mm-40) cc_final: 0.4742 (mm-40) REVERT: O 24 ARG cc_start: 0.5638 (ttp80) cc_final: 0.4810 (tpt90) REVERT: O 120 LYS cc_start: 0.7503 (tptt) cc_final: 0.6980 (mptt) REVERT: P 128 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5153 (mp0) REVERT: G 236 ILE cc_start: 0.6152 (mm) cc_final: 0.5855 (mm) REVERT: G 263 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: H 119 THR cc_start: 0.7469 (t) cc_final: 0.7061 (m) REVERT: H 120 SER cc_start: 0.7423 (OUTLIER) cc_final: 0.6901 (m) REVERT: H 253 LYS cc_start: 0.5533 (mmpt) cc_final: 0.5280 (mtpt) REVERT: H 463 TRP cc_start: 0.3993 (m-10) cc_final: 0.3547 (m100) REVERT: 1 20 TYR cc_start: 0.6100 (t80) cc_final: 0.5433 (t80) REVERT: 1 24 MET cc_start: 0.6326 (mmm) cc_final: 0.5341 (mtp) REVERT: 1 37 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5177 (mm) REVERT: 2 88 MET cc_start: 0.4758 (tpt) cc_final: 0.4360 (mtm) REVERT: 2 98 MET cc_start: 0.6836 (mpp) cc_final: 0.6406 (mpp) REVERT: 2 105 LEU cc_start: 0.4817 (mm) cc_final: 0.4197 (tt) REVERT: 2 108 MET cc_start: 0.5650 (tpp) cc_final: 0.4792 (ptm) REVERT: 3 40 TRP cc_start: 0.4939 (t-100) cc_final: 0.3603 (m-10) REVERT: M 120 LYS cc_start: 0.7687 (tptp) cc_final: 0.7445 (mptt) REVERT: M 127 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.5888 (tpt-90) REVERT: M 188 ARG cc_start: 0.5524 (tpp80) cc_final: 0.5306 (ttm170) REVERT: N 156 TYR cc_start: 0.7175 (t80) cc_final: 0.6795 (t80) REVERT: E 200 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5489 (p90) REVERT: E 270 TYR cc_start: 0.6023 (p90) cc_final: 0.5621 (p90) REVERT: F 366 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7289 (p) REVERT: I 48 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4328 (m-10) REVERT: I 90 TYR cc_start: 0.5562 (m-80) cc_final: 0.5225 (m-80) REVERT: S 16 SER cc_start: 0.4184 (m) cc_final: 0.3474 (p) REVERT: S 20 TYR cc_start: 0.5152 (t80) cc_final: 0.4920 (t80) REVERT: S 71 MET cc_start: 0.4093 (mmt) cc_final: 0.3655 (mmt) REVERT: S 74 ARG cc_start: 0.4413 (ptt180) cc_final: 0.3845 (ttp-110) REVERT: A 344 MET cc_start: 0.6488 (tpp) cc_final: 0.6233 (tpp) REVERT: A 421 ASN cc_start: 0.6755 (m-40) cc_final: 0.6279 (t0) REVERT: B 263 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: B 365 PHE cc_start: 0.6838 (m-10) cc_final: 0.6396 (m-80) REVERT: K 26 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5170 (tt) REVERT: K 27 ARG cc_start: 0.4511 (ptm-80) cc_final: 0.3662 (mtt180) REVERT: K 55 GLU cc_start: 0.5411 (tt0) cc_final: 0.5016 (mm-30) REVERT: L 120 LYS cc_start: 0.7130 (tptt) cc_final: 0.6764 (mmtm) REVERT: V 13 THR cc_start: 0.3972 (m) cc_final: 0.3650 (p) REVERT: V 83 GLU cc_start: 0.4497 (mm-30) cc_final: 0.3439 (mp0) REVERT: W 20 TYR cc_start: 0.5789 (t80) cc_final: 0.5556 (t80) REVERT: W 24 MET cc_start: 0.6436 (mmm) cc_final: 0.5721 (ptm) REVERT: W 71 MET cc_start: 0.5558 (ppp) cc_final: 0.5201 (mmt) REVERT: W 98 MET cc_start: 0.5081 (mmm) cc_final: 0.4879 (mmm) REVERT: X 24 MET cc_start: 0.2688 (OUTLIER) cc_final: 0.1692 (tmm) REVERT: X 108 MET cc_start: 0.5395 (tpp) cc_final: 0.4976 (ptt) REVERT: C 260 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5211 (mt-10) REVERT: C 267 MET cc_start: 0.5474 (mmt) cc_final: 0.5229 (ptm) REVERT: C 367 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6621 (pp30) REVERT: C 421 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.5831 (m-40) REVERT: D 200 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.5223 (p90) REVERT: D 281 LEU cc_start: 0.7249 (mt) cc_final: 0.7044 (mp) REVERT: D 367 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6344 (pp30) outliers start: 266 outliers final: 159 residues processed: 1096 average time/residue: 0.6293 time to fit residues: 1136.7890 Evaluate side-chains 965 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 790 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 1 residue 23 LEU Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain 1 residue 70 ILE Chi-restraints excluded: chain 1 residue 91 SER Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 193 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain X residue 24 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 9.9990 chunk 421 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 562 optimal weight: 0.7980 chunk 595 optimal weight: 6.9990 chunk 293 optimal weight: 0.0170 chunk 533 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 100 GLN 6 97 ASN 7 76 HIS ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 GLN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 311 HIS ** H 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 100 GLN 3 76 HIS ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN F 208 ASN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN I 32 ASN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS J 183 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 387 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN K 66 GLN L 66 GLN W 34 ASN W 76 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 HIS D 353 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 50856 Z= 0.188 Angle : 0.615 13.631 68816 Z= 0.319 Chirality : 0.042 0.226 7576 Planarity : 0.005 0.063 8976 Dihedral : 5.623 31.002 6858 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.54 % Allowed : 15.88 % Favored : 79.58 % 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: -3.02 (0.10), residues: 6128 helix: -1.83 (0.08), residues: 3224 sheet: -3.12 (0.22), residues: 360 loop : -1.86 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 36 HIS 0.014 0.001 HIS J 183 PHE 0.024 0.002 PHE E 346 TYR 0.028 0.001 TYR I 156 ARG 0.006 0.000 ARG 3 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 879 time to evaluate : 6.574 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: 5 88 MET cc_start: 0.2118 (tpp) cc_final: 0.1873 (mmm) REVERT: 5 98 MET cc_start: 0.5451 (mmm) cc_final: 0.4777 (mmm) REVERT: 6 94 GLN cc_start: 0.6395 (mt0) cc_final: 0.6140 (mm110) REVERT: 6 98 MET cc_start: 0.6260 (mmt) cc_final: 0.5936 (mmt) REVERT: 6 102 ARG cc_start: 0.4813 (mmt180) cc_final: 0.4421 (mmt180) REVERT: 7 16 SER cc_start: 0.1873 (m) cc_final: 0.1626 (p) REVERT: 7 24 MET cc_start: 0.6020 (mmm) cc_final: 0.5464 (tpp) REVERT: 7 66 LEU cc_start: 0.6544 (tp) cc_final: 0.6194 (tt) REVERT: 7 80 GLU cc_start: 0.5450 (mm-30) cc_final: 0.5156 (mt-10) REVERT: 8 98 MET cc_start: 0.6823 (tpp) cc_final: 0.6214 (mmt) REVERT: O 24 ARG cc_start: 0.5555 (ttp80) cc_final: 0.4758 (tpt90) REVERT: O 120 LYS cc_start: 0.7293 (tptt) cc_final: 0.6840 (mptt) REVERT: O 172 SER cc_start: 0.6417 (m) cc_final: 0.6034 (t) REVERT: P 48 TYR cc_start: 0.4828 (OUTLIER) cc_final: 0.4547 (m-10) REVERT: P 128 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5078 (mp0) REVERT: G 263 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: G 422 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.4904 (tpt170) REVERT: H 119 THR cc_start: 0.7462 (t) cc_final: 0.7062 (t) REVERT: H 253 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5331 (mtpt) REVERT: 1 24 MET cc_start: 0.6197 (mmm) cc_final: 0.5591 (ptm) REVERT: 1 37 LEU cc_start: 0.5632 (tp) cc_final: 0.4767 (mp) REVERT: 2 83 GLU cc_start: 0.4220 (tp30) cc_final: 0.3102 (tm-30) REVERT: 2 98 MET cc_start: 0.6981 (mpp) cc_final: 0.6562 (mpp) REVERT: 2 105 LEU cc_start: 0.4929 (mm) cc_final: 0.4369 (tt) REVERT: 2 108 MET cc_start: 0.5358 (tpp) cc_final: 0.4767 (ptm) REVERT: 4 94 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6238 (tp40) REVERT: M 120 LYS cc_start: 0.7728 (tptp) cc_final: 0.7490 (mmtt) REVERT: E 200 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5323 (p90) REVERT: E 260 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.4878 (mt-10) REVERT: E 367 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.5986 (pp30) REVERT: F 260 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5395 (mt-10) REVERT: I 48 TYR cc_start: 0.5279 (OUTLIER) cc_final: 0.4302 (m-80) REVERT: J 127 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4412 (ttt180) REVERT: Q 75 GLU cc_start: 0.5735 (tp30) cc_final: 0.5350 (tm-30) REVERT: R 95 GLN cc_start: 0.5370 (mt0) cc_final: 0.5009 (mm-40) REVERT: R 98 MET cc_start: 0.6765 (ttt) cc_final: 0.6055 (mmm) REVERT: S 16 SER cc_start: 0.4157 (m) cc_final: 0.3461 (p) REVERT: S 74 ARG cc_start: 0.4598 (ptt180) cc_final: 0.4094 (ttp-110) REVERT: S 80 GLU cc_start: 0.6004 (mp0) cc_final: 0.5704 (mp0) REVERT: T 83 GLU cc_start: 0.3253 (tp30) cc_final: 0.1877 (tm-30) REVERT: A 260 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.4904 (mt-10) REVERT: A 421 ASN cc_start: 0.6613 (m-40) cc_final: 0.6286 (t0) REVERT: B 147 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6536 (ttmm) REVERT: B 365 PHE cc_start: 0.6797 (m-10) cc_final: 0.6581 (m-80) REVERT: K 26 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5376 (tt) REVERT: K 27 ARG cc_start: 0.4560 (ptm-80) cc_final: 0.3949 (mmm-85) REVERT: L 120 LYS cc_start: 0.7084 (tptt) cc_final: 0.6746 (mmtm) REVERT: U 13 THR cc_start: 0.4294 (p) cc_final: 0.3805 (t) REVERT: V 13 THR cc_start: 0.4006 (m) cc_final: 0.3689 (p) REVERT: V 88 MET cc_start: 0.3638 (mtm) cc_final: 0.3399 (ptp) REVERT: V 98 MET cc_start: 0.6933 (mpp) cc_final: 0.6361 (mpp) REVERT: V 104 HIS cc_start: 0.3443 (t70) cc_final: 0.3134 (t70) REVERT: V 108 MET cc_start: 0.4817 (mmm) cc_final: 0.4500 (mtm) REVERT: W 20 TYR cc_start: 0.5837 (t80) cc_final: 0.5589 (t80) REVERT: W 24 MET cc_start: 0.6567 (mmm) cc_final: 0.5745 (ppp) REVERT: W 66 LEU cc_start: 0.4974 (mp) cc_final: 0.4713 (tt) REVERT: W 71 MET cc_start: 0.6018 (ppp) cc_final: 0.5283 (mmt) REVERT: X 108 MET cc_start: 0.5635 (tpp) cc_final: 0.5195 (ptt) REVERT: C 228 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5918 (mmtt) REVERT: C 421 ASN cc_start: 0.6162 (OUTLIER) cc_final: 0.5794 (t0) REVERT: D 365 PHE cc_start: 0.6832 (m-10) cc_final: 0.6574 (m-80) outliers start: 235 outliers final: 148 residues processed: 1014 average time/residue: 0.6016 time to fit residues: 1014.2020 Evaluate side-chains 928 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 763 time to evaluate : 7.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 422 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 423 VAL Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 1 residue 91 SER Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 10.0000 chunk 337 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 443 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 chunk 508 optimal weight: 5.9990 chunk 411 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 304 optimal weight: 0.9980 chunk 534 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 HIS 7 100 GLN ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 HIS ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 353 ASN 3 76 HIS ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 HIS Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 GLN W 76 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 50856 Z= 0.179 Angle : 0.592 12.605 68816 Z= 0.306 Chirality : 0.041 0.273 7576 Planarity : 0.005 0.054 8976 Dihedral : 5.377 33.261 6858 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.75 % Allowed : 16.07 % Favored : 79.17 % 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: -2.57 (0.10), residues: 6128 helix: -1.45 (0.09), residues: 3264 sheet: -2.89 (0.26), residues: 280 loop : -1.73 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP L 36 HIS 0.021 0.001 HIS J 106 PHE 0.024 0.002 PHE J 146 TYR 0.031 0.001 TYR F 191 ARG 0.006 0.000 ARG 3 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 838 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 98 MET cc_start: 0.5510 (mmm) cc_final: 0.4803 (mmm) REVERT: 6 94 GLN cc_start: 0.6379 (mt0) cc_final: 0.6092 (mm110) REVERT: 6 98 MET cc_start: 0.6196 (mmt) cc_final: 0.5925 (mmt) REVERT: 6 102 ARG cc_start: 0.4814 (mmt180) cc_final: 0.4447 (mmt180) REVERT: 7 24 MET cc_start: 0.5980 (mmm) cc_final: 0.5343 (tpp) REVERT: 7 80 GLU cc_start: 0.5510 (mm-30) cc_final: 0.5287 (mt-10) REVERT: 8 98 MET cc_start: 0.6826 (tpp) cc_final: 0.6218 (mmt) REVERT: O 24 ARG cc_start: 0.5444 (ttp80) cc_final: 0.4646 (tpt90) REVERT: O 172 SER cc_start: 0.6565 (m) cc_final: 0.6189 (t) REVERT: P 48 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4602 (m-10) REVERT: P 128 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5097 (mp0) REVERT: G 191 TYR cc_start: 0.6667 (t80) cc_final: 0.6409 (t80) REVERT: G 260 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5071 (mt-10) REVERT: G 313 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7507 (ptp90) REVERT: G 422 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5009 (ttt180) REVERT: H 119 THR cc_start: 0.7689 (t) cc_final: 0.7280 (t) REVERT: H 195 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.4761 (mmm-85) REVERT: H 253 LYS cc_start: 0.5629 (mmpt) cc_final: 0.5366 (mtpt) REVERT: H 260 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5379 (mt-10) REVERT: H 313 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7383 (ptp90) REVERT: 1 24 MET cc_start: 0.6110 (mmm) cc_final: 0.5111 (mtp) REVERT: 2 9 ASP cc_start: 0.5692 (OUTLIER) cc_final: 0.5235 (p0) REVERT: 2 83 GLU cc_start: 0.3738 (tp30) cc_final: 0.2996 (tm-30) REVERT: 2 88 MET cc_start: 0.4017 (mtm) cc_final: 0.3412 (tpt) REVERT: 2 98 MET cc_start: 0.6757 (mpp) cc_final: 0.6412 (mpp) REVERT: 2 105 LEU cc_start: 0.4846 (mm) cc_final: 0.4318 (tt) REVERT: 2 108 MET cc_start: 0.5196 (tpp) cc_final: 0.4690 (ptm) REVERT: 3 102 ARG cc_start: 0.5067 (mtm110) cc_final: 0.4564 (ptt90) REVERT: 4 94 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.5891 (tp40) REVERT: 4 98 MET cc_start: 0.6412 (ttt) cc_final: 0.6191 (mmt) REVERT: E 200 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.5235 (p90) REVERT: E 260 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.4712 (mt-10) REVERT: E 365 PHE cc_start: 0.7067 (m-10) cc_final: 0.6806 (m-80) REVERT: E 367 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6034 (pp30) REVERT: F 260 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5473 (mt-10) REVERT: I 26 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.4273 (tt) REVERT: I 48 TYR cc_start: 0.5345 (OUTLIER) cc_final: 0.4448 (m-80) REVERT: J 127 ARG cc_start: 0.5120 (OUTLIER) cc_final: 0.4330 (ttt180) REVERT: R 95 GLN cc_start: 0.5500 (mt0) cc_final: 0.5061 (mm-40) REVERT: R 98 MET cc_start: 0.6733 (ttt) cc_final: 0.6072 (mmm) REVERT: S 16 SER cc_start: 0.4149 (m) cc_final: 0.3479 (p) REVERT: S 74 ARG cc_start: 0.4770 (ptt180) cc_final: 0.4152 (ttp-110) REVERT: T 83 GLU cc_start: 0.3234 (tp30) cc_final: 0.1901 (tm-30) REVERT: A 260 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.4959 (mt-10) REVERT: A 421 ASN cc_start: 0.6541 (m-40) cc_final: 0.6224 (t0) REVERT: B 119 THR cc_start: 0.6637 (m) cc_final: 0.6388 (m) REVERT: B 147 LYS cc_start: 0.7006 (ptmt) cc_final: 0.6638 (ptmm) REVERT: K 27 ARG cc_start: 0.4946 (ptm-80) cc_final: 0.4122 (mmm-85) REVERT: K 32 ASN cc_start: 0.6868 (p0) cc_final: 0.6366 (m-40) REVERT: L 120 LYS cc_start: 0.7161 (tptt) cc_final: 0.6856 (mmtm) REVERT: U 41 LEU cc_start: 0.5558 (mm) cc_final: 0.5202 (mt) REVERT: V 13 THR cc_start: 0.4026 (m) cc_final: 0.3659 (p) REVERT: V 104 HIS cc_start: 0.3390 (t70) cc_final: 0.3061 (t70) REVERT: W 66 LEU cc_start: 0.5063 (mp) cc_final: 0.4799 (tt) REVERT: W 71 MET cc_start: 0.6158 (ppp) cc_final: 0.5365 (mmt) REVERT: X 108 MET cc_start: 0.5607 (tpp) cc_final: 0.5176 (ptt) REVERT: C 421 ASN cc_start: 0.6207 (OUTLIER) cc_final: 0.5751 (m-40) REVERT: D 119 THR cc_start: 0.6843 (m) cc_final: 0.6521 (m) REVERT: D 200 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.5023 (p90) REVERT: D 263 GLN cc_start: 0.6490 (tm-30) cc_final: 0.5637 (mp10) REVERT: D 365 PHE cc_start: 0.6858 (m-10) cc_final: 0.6638 (m-80) outliers start: 246 outliers final: 166 residues processed: 978 average time/residue: 0.6046 time to fit residues: 980.6162 Evaluate side-chains 951 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 767 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 422 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 1 residue 91 SER Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 365 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 4.9990 chunk 536 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 596 optimal weight: 1.9990 chunk 494 optimal weight: 30.0000 chunk 275 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 ASN 3 76 HIS ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 97 ASN N 64 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS A 116 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 97 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.7884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 50856 Z= 0.334 Angle : 0.766 14.647 68816 Z= 0.396 Chirality : 0.046 0.256 7576 Planarity : 0.006 0.068 8976 Dihedral : 6.245 35.903 6858 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.72 % Allowed : 16.15 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.81 (0.10), residues: 6128 helix: -1.61 (0.08), residues: 3232 sheet: -2.96 (0.25), residues: 312 loop : -1.87 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP N 36 HIS 0.023 0.002 HIS W 76 PHE 0.033 0.003 PHE B 219 TYR 0.027 0.002 TYR K 156 ARG 0.008 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 819 time to evaluate : 5.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 98 MET cc_start: 0.5202 (mmm) cc_final: 0.4684 (mmm) REVERT: 6 94 GLN cc_start: 0.6378 (mt0) cc_final: 0.6155 (mm110) REVERT: 7 13 THR cc_start: 0.5459 (p) cc_final: 0.5228 (t) REVERT: 7 24 MET cc_start: 0.5620 (mmm) cc_final: 0.5102 (tpp) REVERT: 8 3 LEU cc_start: 0.5722 (tp) cc_final: 0.5255 (mt) REVERT: 8 98 MET cc_start: 0.6749 (tpp) cc_final: 0.6205 (mmt) REVERT: O 20 GLN cc_start: 0.5244 (mm-40) cc_final: 0.4951 (mm110) REVERT: O 48 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5505 (m-10) REVERT: O 120 LYS cc_start: 0.7523 (tptm) cc_final: 0.7152 (mptt) REVERT: O 136 PHE cc_start: 0.6841 (t80) cc_final: 0.6604 (m-80) REVERT: P 128 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: G 200 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.5207 (p90) REVERT: G 260 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5406 (mt-10) REVERT: G 313 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7632 (ptp90) REVERT: H 119 THR cc_start: 0.7840 (t) cc_final: 0.7357 (t) REVERT: H 120 SER cc_start: 0.7164 (OUTLIER) cc_final: 0.6948 (m) REVERT: H 200 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.5260 (p90) REVERT: H 253 LYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5314 (mtpp) REVERT: H 260 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5686 (mt-10) REVERT: 1 24 MET cc_start: 0.6100 (mmm) cc_final: 0.5155 (ptp) REVERT: 2 85 LEU cc_start: 0.5232 (mp) cc_final: 0.4980 (mp) REVERT: 2 88 MET cc_start: 0.4315 (mtm) cc_final: 0.3583 (tpt) REVERT: 2 98 MET cc_start: 0.6764 (mpp) cc_final: 0.6379 (mpp) REVERT: 2 105 LEU cc_start: 0.4802 (mm) cc_final: 0.4257 (tt) REVERT: 2 108 MET cc_start: 0.5184 (tpp) cc_final: 0.4597 (ptm) REVERT: 3 71 MET cc_start: 0.4019 (mtt) cc_final: 0.3804 (mtm) REVERT: 3 102 ARG cc_start: 0.5536 (mtm110) cc_final: 0.4973 (ptt90) REVERT: 4 94 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6168 (tp40) REVERT: 4 98 MET cc_start: 0.6470 (ttt) cc_final: 0.6236 (mmt) REVERT: E 200 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5644 (p90) REVERT: E 260 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5234 (mt-10) REVERT: E 367 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6414 (pp30) REVERT: F 200 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.5270 (p90) REVERT: F 260 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5742 (mt-10) REVERT: F 426 GLU cc_start: 0.5738 (mt-10) cc_final: 0.5304 (mt-10) REVERT: I 26 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4994 (tt) REVERT: I 29 LYS cc_start: 0.5659 (OUTLIER) cc_final: 0.5118 (mmmt) REVERT: I 128 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: J 20 GLN cc_start: 0.5220 (mm-40) cc_final: 0.4898 (mm-40) REVERT: J 127 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.4861 (ttt180) REVERT: R 95 GLN cc_start: 0.5419 (mt0) cc_final: 0.5000 (mm-40) REVERT: R 98 MET cc_start: 0.6749 (ttt) cc_final: 0.5758 (mmm) REVERT: R 102 ARG cc_start: 0.5307 (mtt180) cc_final: 0.5031 (ttt90) REVERT: S 16 SER cc_start: 0.4314 (m) cc_final: 0.3680 (p) REVERT: S 44 PHE cc_start: 0.3092 (m-80) cc_final: 0.2835 (m-80) REVERT: A 200 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.5227 (p90) REVERT: A 260 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5518 (mt-10) REVERT: A 367 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: A 421 ASN cc_start: 0.6862 (m110) cc_final: 0.6310 (t0) REVERT: B 147 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7429 (ttmm) REVERT: B 200 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.5117 (p90) REVERT: B 260 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5690 (mt-10) REVERT: K 25 LYS cc_start: 0.6272 (mtpt) cc_final: 0.5948 (pttp) REVERT: K 27 ARG cc_start: 0.5277 (ptm-80) cc_final: 0.4248 (mmm-85) REVERT: K 32 ASN cc_start: 0.6783 (p0) cc_final: 0.6523 (m-40) REVERT: V 13 THR cc_start: 0.4005 (m) cc_final: 0.3491 (p) REVERT: V 98 MET cc_start: 0.6991 (mpp) cc_final: 0.6547 (mpp) REVERT: V 108 MET cc_start: 0.4021 (mtm) cc_final: 0.3582 (ptp) REVERT: W 24 MET cc_start: 0.6360 (mmm) cc_final: 0.5055 (ptp) REVERT: W 44 PHE cc_start: 0.2220 (m-80) cc_final: 0.1681 (m-80) REVERT: W 66 LEU cc_start: 0.5047 (mp) cc_final: 0.4828 (tt) REVERT: W 71 MET cc_start: 0.6044 (ppp) cc_final: 0.5305 (mmt) REVERT: W 74 ARG cc_start: 0.4834 (ptt180) cc_final: 0.4446 (ttp-110) REVERT: X 83 GLU cc_start: 0.3688 (tp30) cc_final: 0.2218 (tm-30) REVERT: X 108 MET cc_start: 0.5488 (tpp) cc_final: 0.4951 (ptt) REVERT: C 200 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5497 (p90) REVERT: C 260 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5190 (mt-10) REVERT: C 367 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6649 (pp30) REVERT: C 421 ASN cc_start: 0.6299 (OUTLIER) cc_final: 0.5810 (m-40) REVERT: D 200 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5337 (p90) REVERT: D 260 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5435 (mt-10) REVERT: D 365 PHE cc_start: 0.7015 (m-10) cc_final: 0.6638 (m-80) REVERT: D 367 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6561 (pp30) outliers start: 296 outliers final: 210 residues processed: 1006 average time/residue: 0.5998 time to fit residues: 1008.6539 Evaluate side-chains 992 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 751 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain 1 residue 16 SER Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 91 SER Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 160 LYS Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 422 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 339 optimal weight: 7.9990 chunk 435 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 593 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 106 HIS O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 HIS 2 97 ASN 3 76 HIS ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.8158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 50856 Z= 0.253 Angle : 0.682 13.255 68816 Z= 0.353 Chirality : 0.044 0.332 7576 Planarity : 0.005 0.060 8976 Dihedral : 5.909 38.881 6858 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.58 % Allowed : 17.43 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.64 (0.10), residues: 6128 helix: -1.47 (0.09), residues: 3272 sheet: -2.92 (0.25), residues: 312 loop : -1.78 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 36 HIS 0.018 0.001 HIS B 387 PHE 0.026 0.002 PHE J 146 TYR 0.031 0.002 TYR C 191 ARG 0.006 0.001 ARG 3 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 796 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 37 LEU cc_start: 0.5675 (mt) cc_final: 0.5133 (mp) REVERT: 5 53 GLU cc_start: 0.3680 (tp30) cc_final: 0.3408 (tp30) REVERT: 5 98 MET cc_start: 0.5160 (mmm) cc_final: 0.4693 (mmm) REVERT: 7 13 THR cc_start: 0.5401 (p) cc_final: 0.5198 (t) REVERT: 7 24 MET cc_start: 0.6150 (mmm) cc_final: 0.5437 (tpp) REVERT: 7 41 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4792 (mm) REVERT: 8 3 LEU cc_start: 0.5936 (tp) cc_final: 0.5411 (mt) REVERT: 8 98 MET cc_start: 0.6629 (tpp) cc_final: 0.6080 (mmt) REVERT: O 20 GLN cc_start: 0.5194 (mm-40) cc_final: 0.4855 (mm-40) REVERT: O 24 ARG cc_start: 0.5271 (ttp80) cc_final: 0.4892 (ttp80) REVERT: O 48 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.5376 (m-10) REVERT: O 120 LYS cc_start: 0.7499 (tptm) cc_final: 0.7067 (mptt) REVERT: O 172 SER cc_start: 0.6386 (m) cc_final: 0.5998 (t) REVERT: P 120 LYS cc_start: 0.7819 (tptt) cc_final: 0.7605 (tptp) REVERT: P 128 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: G 200 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5084 (p90) REVERT: G 260 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.4981 (mt-10) REVERT: G 422 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5147 (tpt170) REVERT: G 463 TRP cc_start: 0.3847 (m-10) cc_final: 0.3547 (m100) REVERT: H 200 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5376 (p90) REVERT: H 253 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5289 (mtpp) REVERT: H 260 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5345 (mt-10) REVERT: H 313 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7397 (ptp90) REVERT: 1 24 MET cc_start: 0.6146 (mmm) cc_final: 0.5214 (ptp) REVERT: 1 71 MET cc_start: 0.3923 (mmm) cc_final: 0.3272 (mmm) REVERT: 2 83 GLU cc_start: 0.3953 (tp30) cc_final: 0.3063 (tm-30) REVERT: 2 85 LEU cc_start: 0.5308 (mp) cc_final: 0.4924 (mp) REVERT: 2 88 MET cc_start: 0.4345 (mtm) cc_final: 0.3646 (tpt) REVERT: 2 98 MET cc_start: 0.6863 (mpp) cc_final: 0.6520 (mpp) REVERT: 2 105 LEU cc_start: 0.4733 (mm) cc_final: 0.4017 (tp) REVERT: 2 108 MET cc_start: 0.5145 (tpp) cc_final: 0.4514 (ptm) REVERT: 3 102 ARG cc_start: 0.5397 (mtm110) cc_final: 0.5034 (ptt90) REVERT: 4 94 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6155 (tp40) REVERT: E 200 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5545 (p90) REVERT: E 260 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5368 (mt-10) REVERT: E 365 PHE cc_start: 0.7110 (m-10) cc_final: 0.6860 (m-80) REVERT: E 367 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6247 (pp30) REVERT: F 260 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5580 (mt-10) REVERT: F 426 GLU cc_start: 0.5703 (mt-10) cc_final: 0.5270 (mt-10) REVERT: I 26 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4900 (tt) REVERT: I 48 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4121 (m-10) REVERT: J 127 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4689 (ttt180) REVERT: J 172 SER cc_start: 0.6365 (m) cc_final: 0.6115 (t) REVERT: R 95 GLN cc_start: 0.5428 (mt0) cc_final: 0.5052 (mm-40) REVERT: R 98 MET cc_start: 0.6704 (ttt) cc_final: 0.5742 (mmm) REVERT: S 16 SER cc_start: 0.4328 (m) cc_final: 0.3810 (p) REVERT: S 21 GLN cc_start: 0.4670 (mm-40) cc_final: 0.4385 (mm-40) REVERT: T 83 GLU cc_start: 0.3064 (tp30) cc_final: 0.2773 (tp30) REVERT: A 200 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5074 (p90) REVERT: A 260 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5337 (mt-10) REVERT: A 367 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6868 (pt0) REVERT: A 421 ASN cc_start: 0.6585 (m110) cc_final: 0.6115 (t0) REVERT: B 147 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7132 (ttmm) REVERT: B 200 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5078 (p90) REVERT: B 260 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5558 (mt-10) REVERT: K 25 LYS cc_start: 0.6408 (mtpt) cc_final: 0.6051 (pttp) REVERT: K 27 ARG cc_start: 0.5198 (ptm-80) cc_final: 0.4324 (mmm-85) REVERT: K 129 ILE cc_start: 0.6405 (mm) cc_final: 0.6179 (tt) REVERT: U 13 THR cc_start: 0.4789 (p) cc_final: 0.4408 (t) REVERT: V 13 THR cc_start: 0.3848 (m) cc_final: 0.3551 (p) REVERT: V 108 MET cc_start: 0.3670 (mtm) cc_final: 0.3334 (ptp) REVERT: W 24 MET cc_start: 0.6248 (mmm) cc_final: 0.5041 (ptp) REVERT: W 44 PHE cc_start: 0.2263 (m-80) cc_final: 0.1674 (m-80) REVERT: W 71 MET cc_start: 0.5876 (ppp) cc_final: 0.5312 (mmt) REVERT: W 74 ARG cc_start: 0.4738 (ptt180) cc_final: 0.4481 (ttp-110) REVERT: X 83 GLU cc_start: 0.3567 (tp30) cc_final: 0.2417 (tm-30) REVERT: X 108 MET cc_start: 0.5207 (tpp) cc_final: 0.4776 (ptt) REVERT: C 200 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5310 (p90) REVERT: C 260 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5625 (mt-10) REVERT: C 367 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6612 (pp30) REVERT: C 421 ASN cc_start: 0.6181 (OUTLIER) cc_final: 0.5723 (m-40) REVERT: D 200 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5294 (p90) REVERT: D 260 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5262 (mt-10) REVERT: D 348 ASP cc_start: 0.6871 (m-30) cc_final: 0.6657 (m-30) REVERT: D 365 PHE cc_start: 0.6864 (m-10) cc_final: 0.6623 (m-80) REVERT: D 367 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6522 (pp30) outliers start: 289 outliers final: 215 residues processed: 974 average time/residue: 0.5871 time to fit residues: 953.1658 Evaluate side-chains 1007 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 762 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 41 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain 7 residue 93 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 422 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 1 residue 16 SER Chi-restraints excluded: chain 1 residue 91 SER Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 354 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 377 optimal weight: 0.0030 chunk 404 optimal weight: 0.3980 chunk 293 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 466 optimal weight: 10.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 100 GLN 3 76 HIS 4 15 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 97 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.8362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 50856 Z= 0.188 Angle : 0.613 12.313 68816 Z= 0.316 Chirality : 0.042 0.280 7576 Planarity : 0.005 0.053 8976 Dihedral : 5.440 34.461 6855 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.93 % Allowed : 18.22 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 6128 helix: -1.11 (0.09), residues: 3224 sheet: -2.62 (0.27), residues: 280 loop : -1.68 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 36 HIS 0.015 0.001 HIS B 387 PHE 0.021 0.002 PHE J 146 TYR 0.025 0.001 TYR H 86 ARG 0.007 0.000 ARG 3 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 804 time to evaluate : 6.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 37 LEU cc_start: 0.5839 (mt) cc_final: 0.5316 (mp) REVERT: 5 93 ILE cc_start: 0.2910 (mt) cc_final: 0.2530 (tp) REVERT: 5 98 MET cc_start: 0.4978 (mmm) cc_final: 0.4522 (mmm) REVERT: 6 98 MET cc_start: 0.6389 (mmt) cc_final: 0.6167 (mmt) REVERT: 6 102 ARG cc_start: 0.4903 (mmt180) cc_final: 0.4626 (mmt180) REVERT: 7 13 THR cc_start: 0.5619 (p) cc_final: 0.5414 (t) REVERT: 7 24 MET cc_start: 0.6190 (mmm) cc_final: 0.5501 (tpp) REVERT: 7 41 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4870 (mm) REVERT: 8 3 LEU cc_start: 0.5991 (tp) cc_final: 0.5345 (mt) REVERT: 8 98 MET cc_start: 0.6618 (tpp) cc_final: 0.6066 (mpp) REVERT: O 24 ARG cc_start: 0.5406 (ttp80) cc_final: 0.4749 (tpm170) REVERT: O 120 LYS cc_start: 0.7497 (tptm) cc_final: 0.6958 (mptt) REVERT: O 172 SER cc_start: 0.6532 (m) cc_final: 0.6138 (t) REVERT: P 160 LYS cc_start: 0.7555 (pttm) cc_final: 0.7200 (pttm) REVERT: G 200 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5157 (p90) REVERT: G 244 THR cc_start: 0.8446 (t) cc_final: 0.8217 (m) REVERT: G 260 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.4898 (mt-10) REVERT: G 463 TRP cc_start: 0.3803 (m-10) cc_final: 0.3293 (m-10) REVERT: H 195 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5205 (mmm-85) REVERT: H 200 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5351 (p90) REVERT: H 253 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.5478 (mtpp) REVERT: H 260 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5488 (mt-10) REVERT: H 313 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7307 (ptp90) REVERT: 1 24 MET cc_start: 0.6179 (mmm) cc_final: 0.5230 (ptp) REVERT: 1 71 MET cc_start: 0.3805 (mmm) cc_final: 0.3218 (mmm) REVERT: 2 9 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5187 (p0) REVERT: 2 71 MET cc_start: 0.0005 (tpt) cc_final: -0.0288 (mmm) REVERT: 2 83 GLU cc_start: 0.3966 (tp30) cc_final: 0.3013 (tm-30) REVERT: 2 85 LEU cc_start: 0.5316 (mp) cc_final: 0.4938 (mp) REVERT: 2 88 MET cc_start: 0.4324 (mtm) cc_final: 0.3579 (tpt) REVERT: 2 98 MET cc_start: 0.6754 (mpp) cc_final: 0.6381 (mpp) REVERT: 2 105 LEU cc_start: 0.4656 (mm) cc_final: 0.4103 (tt) REVERT: 2 108 MET cc_start: 0.4986 (tpp) cc_final: 0.4344 (ptm) REVERT: 3 69 ARG cc_start: 0.5998 (ttt-90) cc_final: 0.5650 (ttt-90) REVERT: 3 74 ARG cc_start: 0.4733 (ptt180) cc_final: 0.3966 (tmm-80) REVERT: 3 102 ARG cc_start: 0.5360 (mtm110) cc_final: 0.4958 (ptt90) REVERT: 4 94 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6279 (tp40) REVERT: 4 100 GLN cc_start: 0.3542 (mt0) cc_final: 0.3203 (mp10) REVERT: M 134 LYS cc_start: 0.7733 (tptp) cc_final: 0.7265 (tttt) REVERT: N 120 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6899 (mttp) REVERT: E 200 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5488 (p90) REVERT: E 260 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5158 (mt-10) REVERT: E 367 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6292 (pp30) REVERT: F 260 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5546 (mt-10) REVERT: F 426 GLU cc_start: 0.5541 (mt-10) cc_final: 0.5135 (mt-10) REVERT: I 26 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4951 (tt) REVERT: I 48 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.4043 (m-10) REVERT: J 127 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.4560 (ttt180) REVERT: J 172 SER cc_start: 0.6366 (m) cc_final: 0.6150 (t) REVERT: Q 60 PHE cc_start: 0.2021 (OUTLIER) cc_final: 0.1439 (m-80) REVERT: R 95 GLN cc_start: 0.5543 (mt0) cc_final: 0.5113 (mm-40) REVERT: R 98 MET cc_start: 0.5959 (ttt) cc_final: 0.5622 (mmm) REVERT: S 16 SER cc_start: 0.4325 (m) cc_final: 0.3811 (p) REVERT: S 76 HIS cc_start: 0.5766 (OUTLIER) cc_final: 0.4795 (t-170) REVERT: T 83 GLU cc_start: 0.3300 (tp30) cc_final: 0.1543 (tm-30) REVERT: A 200 PHE cc_start: 0.5785 (OUTLIER) cc_final: 0.4995 (p90) REVERT: A 260 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5055 (mt-10) REVERT: A 367 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: A 421 ASN cc_start: 0.6563 (m110) cc_final: 0.6121 (m-40) REVERT: B 38 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5616 (tt) REVERT: B 200 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.4924 (p90) REVERT: B 281 LEU cc_start: 0.7154 (mt) cc_final: 0.6935 (mp) REVERT: K 25 LYS cc_start: 0.6491 (mtpt) cc_final: 0.6071 (pttp) REVERT: K 27 ARG cc_start: 0.5080 (ptm-80) cc_final: 0.4254 (mmm-85) REVERT: U 13 THR cc_start: 0.4906 (p) cc_final: 0.4494 (t) REVERT: V 13 THR cc_start: 0.3982 (m) cc_final: 0.3660 (p) REVERT: W 24 MET cc_start: 0.6199 (mmm) cc_final: 0.4967 (ptp) REVERT: W 44 PHE cc_start: 0.2051 (m-80) cc_final: 0.1618 (m-80) REVERT: W 71 MET cc_start: 0.5594 (ppp) cc_final: 0.5389 (mmt) REVERT: X 83 GLU cc_start: 0.3105 (tp30) cc_final: 0.1963 (tm-30) REVERT: X 108 MET cc_start: 0.5279 (tpp) cc_final: 0.4748 (ptt) REVERT: C 200 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5222 (p90) REVERT: C 260 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5532 (mt-10) REVERT: C 421 ASN cc_start: 0.5934 (OUTLIER) cc_final: 0.5546 (m-40) REVERT: D 200 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5251 (p90) REVERT: D 367 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6468 (pp30) outliers start: 255 outliers final: 193 residues processed: 967 average time/residue: 0.5909 time to fit residues: 949.3319 Evaluate side-chains 969 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 748 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 41 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 310 ILE Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 288 ASN Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 1 residue 16 SER Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 20.0000 chunk 568 optimal weight: 0.9990 chunk 518 optimal weight: 30.0000 chunk 553 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 434 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 499 optimal weight: 2.9990 chunk 523 optimal weight: 40.0000 chunk 551 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 97 ASN 6 104 HIS 7 76 HIS 7 100 GLN O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS ** 3 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 104 HIS N 183 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS Q 76 HIS ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.8503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 50856 Z= 0.178 Angle : 0.603 12.450 68816 Z= 0.310 Chirality : 0.042 0.262 7576 Planarity : 0.005 0.059 8976 Dihedral : 5.297 34.708 6855 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.64 % Allowed : 18.70 % Favored : 76.66 % 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: -1.98 (0.10), residues: 6128 helix: -0.89 (0.09), residues: 3232 sheet: -2.40 (0.27), residues: 280 loop : -1.60 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 36 HIS 0.024 0.001 HIS S 76 PHE 0.021 0.002 PHE J 146 TYR 0.035 0.001 TYR K 156 ARG 0.017 0.000 ARG 6 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 790 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 37 LEU cc_start: 0.5801 (mt) cc_final: 0.5247 (mp) REVERT: 5 93 ILE cc_start: 0.2975 (mt) cc_final: 0.2595 (tp) REVERT: 5 98 MET cc_start: 0.4945 (mmm) cc_final: 0.4498 (mmm) REVERT: 6 102 ARG cc_start: 0.4969 (mmt180) cc_final: 0.4499 (mmt180) REVERT: 7 13 THR cc_start: 0.5600 (p) cc_final: 0.5294 (t) REVERT: 7 24 MET cc_start: 0.5943 (mmm) cc_final: 0.5347 (tpp) REVERT: 7 41 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.4934 (mm) REVERT: 8 3 LEU cc_start: 0.5990 (tp) cc_final: 0.5364 (mt) REVERT: 8 98 MET cc_start: 0.6534 (tpp) cc_final: 0.6006 (mpp) REVERT: O 20 GLN cc_start: 0.5156 (mm-40) cc_final: 0.4818 (mm-40) REVERT: O 24 ARG cc_start: 0.5392 (ttp80) cc_final: 0.4714 (tpm170) REVERT: O 172 SER cc_start: 0.6551 (m) cc_final: 0.6173 (t) REVERT: P 120 LYS cc_start: 0.7859 (tptt) cc_final: 0.7622 (tptt) REVERT: G 200 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5208 (p90) REVERT: G 244 THR cc_start: 0.8383 (t) cc_final: 0.8178 (m) REVERT: G 260 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.4875 (mt-10) REVERT: G 463 TRP cc_start: 0.3746 (m-10) cc_final: 0.3269 (m-10) REVERT: H 195 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5193 (mmm-85) REVERT: H 200 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5168 (p90) REVERT: H 253 LYS cc_start: 0.5715 (OUTLIER) cc_final: 0.5502 (mtpp) REVERT: H 260 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5118 (mt-10) REVERT: H 313 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7304 (ptp90) REVERT: 1 24 MET cc_start: 0.6251 (mmm) cc_final: 0.5281 (ptp) REVERT: 2 9 ASP cc_start: 0.5533 (OUTLIER) cc_final: 0.5190 (p0) REVERT: 2 83 GLU cc_start: 0.3964 (tp30) cc_final: 0.3020 (tm-30) REVERT: 2 85 LEU cc_start: 0.5300 (mp) cc_final: 0.4906 (mp) REVERT: 2 88 MET cc_start: 0.4326 (mtm) cc_final: 0.3586 (tpt) REVERT: 2 98 MET cc_start: 0.6748 (mpp) cc_final: 0.6364 (mpp) REVERT: 2 105 LEU cc_start: 0.4602 (mm) cc_final: 0.4058 (tt) REVERT: 2 108 MET cc_start: 0.4969 (tpp) cc_final: 0.4315 (ptm) REVERT: 3 69 ARG cc_start: 0.5768 (ttt-90) cc_final: 0.5398 (ttt-90) REVERT: 3 74 ARG cc_start: 0.4846 (ptt180) cc_final: 0.3965 (tmm-80) REVERT: 3 102 ARG cc_start: 0.5388 (mtm110) cc_final: 0.5008 (ptt90) REVERT: 4 94 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6219 (tp40) REVERT: 4 100 GLN cc_start: 0.3493 (mt0) cc_final: 0.3217 (mp10) REVERT: M 156 TYR cc_start: 0.6706 (t80) cc_final: 0.6273 (t80) REVERT: N 55 GLU cc_start: 0.5719 (tt0) cc_final: 0.5162 (mm-30) REVERT: N 160 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7533 (ptpp) REVERT: E 200 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5361 (p90) REVERT: E 260 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.4773 (mt-10) REVERT: E 367 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: F 260 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5315 (mt-10) REVERT: F 426 GLU cc_start: 0.5584 (mt-10) cc_final: 0.5191 (mt-10) REVERT: I 26 LEU cc_start: 0.5253 (OUTLIER) cc_final: 0.4993 (tt) REVERT: I 48 TYR cc_start: 0.4719 (OUTLIER) cc_final: 0.3984 (m-10) REVERT: J 90 TYR cc_start: 0.5688 (m-80) cc_final: 0.5281 (m-80) REVERT: J 127 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.4535 (ttt180) REVERT: J 172 SER cc_start: 0.6314 (m) cc_final: 0.5706 (t) REVERT: R 24 MET cc_start: 0.1928 (mmm) cc_final: 0.0334 (tpt) REVERT: R 95 GLN cc_start: 0.5545 (mt0) cc_final: 0.5111 (mm-40) REVERT: R 98 MET cc_start: 0.5949 (ttt) cc_final: 0.5621 (mmm) REVERT: S 16 SER cc_start: 0.3976 (m) cc_final: 0.3485 (p) REVERT: S 76 HIS cc_start: 0.5850 (m-70) cc_final: 0.5385 (t-170) REVERT: T 83 GLU cc_start: 0.3561 (tp30) cc_final: 0.1898 (tm-30) REVERT: T 98 MET cc_start: 0.6556 (ttt) cc_final: 0.6208 (mmt) REVERT: A 200 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.4935 (p90) REVERT: A 260 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5004 (mt-10) REVERT: A 367 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: A 421 ASN cc_start: 0.6755 (m110) cc_final: 0.6254 (m-40) REVERT: B 38 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5597 (tt) REVERT: B 200 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.5051 (p90) REVERT: B 260 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5034 (mt-10) REVERT: K 27 ARG cc_start: 0.5046 (ptm-80) cc_final: 0.4254 (mmm-85) REVERT: U 13 THR cc_start: 0.4878 (p) cc_final: 0.4462 (t) REVERT: V 13 THR cc_start: 0.3912 (m) cc_final: 0.3587 (p) REVERT: W 24 MET cc_start: 0.6317 (mmm) cc_final: 0.5087 (ptp) REVERT: W 44 PHE cc_start: 0.2319 (m-80) cc_final: 0.1772 (m-80) REVERT: X 108 MET cc_start: 0.5218 (tpp) cc_final: 0.4761 (ptt) REVERT: C 200 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5275 (p90) REVERT: C 260 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5495 (mt-10) REVERT: C 367 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6666 (pp30) REVERT: C 388 MET cc_start: 0.6930 (mmt) cc_final: 0.6577 (tpp) REVERT: D 200 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.5140 (p90) REVERT: D 367 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6511 (pp30) outliers start: 240 outliers final: 192 residues processed: 946 average time/residue: 0.5825 time to fit residues: 918.2278 Evaluate side-chains 972 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 753 time to evaluate : 5.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 41 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 20.0000 chunk 585 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 613 optimal weight: 9.9990 chunk 564 optimal weight: 8.9990 chunk 488 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 97 ASN 6 104 HIS O 148 ASN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS 3 94 GLN ** 3 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 295 HIS ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 97 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.8684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 50856 Z= 0.274 Angle : 0.706 12.757 68816 Z= 0.365 Chirality : 0.045 0.246 7576 Planarity : 0.005 0.054 8976 Dihedral : 5.850 35.142 6855 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.91 % Allowed : 18.89 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.27 (0.10), residues: 6128 helix: -1.14 (0.09), residues: 3256 sheet: -2.58 (0.26), residues: 312 loop : -1.70 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP L 36 HIS 0.014 0.002 HIS B 387 PHE 0.027 0.003 PHE C 109 TYR 0.037 0.002 TYR K 156 ARG 0.012 0.001 ARG 6 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 766 time to evaluate : 5.800 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: 5 37 LEU cc_start: 0.5747 (mt) cc_final: 0.5157 (mp) REVERT: 5 74 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.2978 (ptp-170) REVERT: 5 93 ILE cc_start: 0.2829 (mt) cc_final: 0.2489 (tp) REVERT: 5 98 MET cc_start: 0.4873 (mmm) cc_final: 0.4654 (mmm) REVERT: 6 102 ARG cc_start: 0.4956 (mmt180) cc_final: 0.4557 (mmt180) REVERT: 7 13 THR cc_start: 0.5553 (p) cc_final: 0.5251 (t) REVERT: 7 24 MET cc_start: 0.5806 (mmm) cc_final: 0.4882 (tpp) REVERT: 8 3 LEU cc_start: 0.6101 (tp) cc_final: 0.5507 (mt) REVERT: 8 98 MET cc_start: 0.6625 (tpp) cc_final: 0.6086 (mpp) REVERT: O 20 GLN cc_start: 0.5199 (mm-40) cc_final: 0.4890 (mm110) REVERT: O 24 ARG cc_start: 0.5348 (ttp80) cc_final: 0.4956 (ttp80) REVERT: O 120 LYS cc_start: 0.7513 (tptm) cc_final: 0.7129 (mptt) REVERT: P 120 LYS cc_start: 0.7859 (tptt) cc_final: 0.7655 (tptt) REVERT: G 200 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.4912 (p90) REVERT: G 244 THR cc_start: 0.8441 (t) cc_final: 0.8233 (m) REVERT: G 260 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5085 (mt-10) REVERT: G 367 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6502 (pp30) REVERT: G 463 TRP cc_start: 0.3699 (m-10) cc_final: 0.3230 (m-10) REVERT: H 195 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5337 (mmm-85) REVERT: H 200 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.5282 (p90) REVERT: H 253 LYS cc_start: 0.5685 (OUTLIER) cc_final: 0.5331 (mtpp) REVERT: H 260 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5610 (mt-10) REVERT: 1 24 MET cc_start: 0.6345 (mmm) cc_final: 0.5281 (ptp) REVERT: 2 83 GLU cc_start: 0.4107 (tp30) cc_final: 0.3197 (tm-30) REVERT: 2 85 LEU cc_start: 0.5279 (mp) cc_final: 0.4863 (mp) REVERT: 2 88 MET cc_start: 0.4280 (mtm) cc_final: 0.3580 (tpt) REVERT: 2 98 MET cc_start: 0.6783 (mpp) cc_final: 0.6357 (mpp) REVERT: 2 105 LEU cc_start: 0.4621 (mm) cc_final: 0.4107 (mp) REVERT: 2 108 MET cc_start: 0.4808 (tpp) cc_final: 0.4197 (ptm) REVERT: 3 69 ARG cc_start: 0.5995 (ttt-90) cc_final: 0.5627 (ttt-90) REVERT: 3 74 ARG cc_start: 0.4970 (ptt180) cc_final: 0.3913 (tmm-80) REVERT: 3 102 ARG cc_start: 0.5600 (mtm110) cc_final: 0.4987 (ptt90) REVERT: 4 108 MET cc_start: 0.2848 (mmp) cc_final: 0.2368 (ptp) REVERT: N 55 GLU cc_start: 0.5433 (tt0) cc_final: 0.4985 (mm-30) REVERT: N 160 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7555 (ptpp) REVERT: E 200 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5508 (p90) REVERT: E 260 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5303 (mt-10) REVERT: E 367 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6592 (pp30) REVERT: F 200 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5216 (p90) REVERT: F 260 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5744 (mt-10) REVERT: F 426 GLU cc_start: 0.5714 (mt-10) cc_final: 0.5349 (mt-10) REVERT: I 48 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.4472 (m-10) REVERT: J 20 GLN cc_start: 0.5344 (mm-40) cc_final: 0.5100 (mm-40) REVERT: J 127 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.4792 (ttt180) REVERT: J 172 SER cc_start: 0.5976 (m) cc_final: 0.5765 (t) REVERT: R 24 MET cc_start: 0.2036 (mmm) cc_final: 0.0513 (tpt) REVERT: R 95 GLN cc_start: 0.5620 (mt0) cc_final: 0.5167 (mm-40) REVERT: S 16 SER cc_start: 0.4455 (m) cc_final: 0.4050 (p) REVERT: S 76 HIS cc_start: 0.5750 (m-70) cc_final: 0.5078 (t-170) REVERT: T 83 GLU cc_start: 0.3457 (tp30) cc_final: 0.1896 (tm-30) REVERT: T 98 MET cc_start: 0.6429 (ttt) cc_final: 0.6186 (mmt) REVERT: A 200 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.4893 (p90) REVERT: A 260 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5229 (mt-10) REVERT: A 367 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6803 (pt0) REVERT: B 200 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.5114 (p90) REVERT: B 260 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5441 (mt-10) REVERT: K 27 ARG cc_start: 0.5220 (ptm-80) cc_final: 0.4335 (mmm-85) REVERT: L 42 SER cc_start: 0.5127 (t) cc_final: 0.4888 (m) REVERT: V 13 THR cc_start: 0.3971 (m) cc_final: 0.3660 (p) REVERT: W 24 MET cc_start: 0.6429 (mmm) cc_final: 0.5045 (ptp) REVERT: W 74 ARG cc_start: 0.4994 (ptt180) cc_final: 0.3972 (tmm-80) REVERT: X 108 MET cc_start: 0.4915 (tpp) cc_final: 0.4502 (ptt) REVERT: C 200 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5317 (p90) REVERT: C 260 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5485 (mt-10) REVERT: C 367 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6694 (pp30) REVERT: C 421 ASN cc_start: 0.5938 (OUTLIER) cc_final: 0.5561 (m-40) REVERT: D 200 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5134 (p90) REVERT: D 367 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6543 (pp30) outliers start: 254 outliers final: 204 residues processed: 927 average time/residue: 0.5801 time to fit residues: 898.5356 Evaluate side-chains 968 residues out of total 5192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 738 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 74 ARG Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain 7 residue 93 ILE Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 137 SER Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 367 GLN Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain 1 residue 16 SER Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 14 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 3.9990 chunk 520 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 450 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 489 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 502 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 21 GLN 6 97 ASN 6 104 HIS O 148 ASN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS ** 3 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 97 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.241564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.215345 restraints weight = 78183.769| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 1.53 r_work: 0.4495 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4410 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.8782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 50856 Z= 0.206 Angle : 0.640 12.251 68816 Z= 0.330 Chirality : 0.043 0.254 7576 Planarity : 0.005 0.063 8976 Dihedral : 5.530 36.013 6852 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.52 % Allowed : 19.38 % Favored : 76.10 % 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: -2.09 (0.10), residues: 6128 helix: -0.98 (0.09), residues: 3288 sheet: -2.05 (0.33), residues: 192 loop : -1.75 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 7 40 HIS 0.013 0.001 HIS B 387 PHE 0.038 0.002 PHE Q 60 TYR 0.031 0.002 TYR I 156 ARG 0.010 0.000 ARG 6 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16341.95 seconds wall clock time: 294 minutes 59.04 seconds (17699.04 seconds total)