Starting phenix.real_space_refine on Thu Feb 22 08:47:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yi5_6830/02_2024/5yi5_6830.pdb" } resolution = 3.0 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= 0.021 sd= 0.084 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 21216 2.51 5 N 5928 2.21 5 O 6504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 16.26, per 1000 atoms: 0.48 Number of scatterers: 33816 At special positions: 0 Unit cell: (139.73, 138.333, 141.127, 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 6504 8.00 N 5928 7.00 C 21216 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: 12.28 Conformation dependent library (CDL) restraints added in 6.6 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 62 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 173 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 175 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 62 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 173 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 175 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 62 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 175 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 37 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS F 144 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 173 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 175 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU G 62 " --> pdb=" O HIS G 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 175 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU H 62 " --> pdb=" O HIS H 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS H 103 " --> pdb=" O ASN H 99 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS H 144 " --> pdb=" O ASN H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 173 " --> pdb=" O TYR H 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 175 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 177 " --> pdb=" O LYS H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU I 62 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS I 103 " --> pdb=" O ASN I 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR I 138 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS I 144 " --> pdb=" O ASN I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 173 " --> pdb=" O TYR I 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 175 " --> pdb=" O PHE I 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY I 177 " --> pdb=" O LYS I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS J 103 " --> pdb=" O ASN J 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR J 138 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS J 144 " --> pdb=" O ASN J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS J 173 " --> pdb=" O TYR J 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 175 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU K 36 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER K 37 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS K 54 " --> pdb=" O LYS K 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU K 62 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS K 103 " --> pdb=" O ASN K 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR K 138 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS K 144 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS K 173 " --> pdb=" O TYR K 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 175 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY K 177 " --> pdb=" O LYS K 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER L 37 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS L 54 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU L 62 " --> pdb=" O HIS L 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR L 138 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS L 144 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 173 " --> pdb=" O TYR L 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 175 " --> pdb=" O PHE L 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY L 177 " --> pdb=" O LYS L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 36 " --> pdb=" O SER M 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER M 37 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS M 54 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU M 62 " --> pdb=" O HIS M 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS M 103 " --> pdb=" O ASN M 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR M 138 " --> pdb=" O ILE M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS M 144 " --> pdb=" O ASN M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS M 173 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR M 175 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER N 37 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU N 62 " --> pdb=" O HIS N 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN N 76 " --> pdb=" O LYS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS N 103 " --> pdb=" O ASN N 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR N 138 " --> pdb=" O ILE N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS N 144 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS N 173 " --> pdb=" O TYR N 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR N 175 " --> pdb=" O PHE N 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY N 177 " --> pdb=" O LYS N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER O 37 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU O 62 " --> pdb=" O HIS O 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN O 76 " --> pdb=" O LYS O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS O 103 " --> pdb=" O ASN O 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR O 138 " --> pdb=" O ILE O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS O 144 " --> pdb=" O ASN O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS O 173 " --> pdb=" O TYR O 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 175 " --> pdb=" O PHE O 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY O 177 " --> pdb=" O LYS O 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN P 22 " --> pdb=" O GLU P 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU P 36 " --> pdb=" O SER P 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER P 37 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU P 62 " --> pdb=" O HIS P 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET P 71 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS P 103 " --> pdb=" O ASN P 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS P 125 " --> pdb=" O LEU P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR P 138 " --> pdb=" O ILE P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS P 173 " --> pdb=" O TYR P 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR P 175 " --> pdb=" O PHE P 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER Q 37 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Q 62 " --> pdb=" O HIS Q 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN Q 76 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS Q 103 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN Q 110 " --> pdb=" O HIS Q 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Q 125 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR Q 138 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Q 144 " --> pdb=" O ASN Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS Q 173 " --> pdb=" O TYR Q 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR Q 175 " --> pdb=" O PHE Q 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY Q 177 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER R 37 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU R 62 " --> pdb=" O HIS R 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS R 103 " --> pdb=" O ASN R 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 removed outlier: 3.816A pdb=" N TYR R 138 " --> pdb=" O ILE R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS R 144 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS R 173 " --> pdb=" O TYR R 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN S 22 " --> pdb=" O GLU S 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG S 23 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU S 36 " --> pdb=" O SER S 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU S 62 " --> pdb=" O HIS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN S 76 " --> pdb=" O LYS S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS S 103 " --> pdb=" O ASN S 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS S 125 " --> pdb=" O LEU S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR S 138 " --> pdb=" O ILE S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS S 144 " --> pdb=" O ASN S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS S 173 " --> pdb=" O TYR S 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR S 175 " --> pdb=" O PHE S 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY S 177 " --> pdb=" O LYS S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU T 36 " --> pdb=" O SER T 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER T 37 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS T 61 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU T 62 " --> pdb=" O HIS T 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS T 103 " --> pdb=" O ASN T 99 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS T 125 " --> pdb=" O LEU T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR T 138 " --> pdb=" O ILE T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 160 removed outlier: 3.553A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS T 144 " --> pdb=" O ASN T 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T 173 " --> pdb=" O TYR T 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR T 175 " --> pdb=" O PHE T 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG U 23 " --> pdb=" O ALA U 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU U 36 " --> pdb=" O SER U 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 77 removed outlier: 3.998A pdb=" N ALA U 53 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU U 62 " --> pdb=" O HIS U 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET U 71 " --> pdb=" O ALA U 67 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS U 103 " --> pdb=" O ASN U 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS U 125 " --> pdb=" O LEU U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR U 138 " --> pdb=" O ILE U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS U 144 " --> pdb=" O ASN U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS U 173 " --> pdb=" O TYR U 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR U 175 " --> pdb=" O PHE U 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY U 177 " --> pdb=" O LYS U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN V 22 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU V 36 " --> pdb=" O SER V 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER V 37 " --> pdb=" O TYR V 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS V 54 " --> pdb=" O LYS V 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS V 61 " --> pdb=" O LEU V 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU V 62 " --> pdb=" O HIS V 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET V 71 " --> pdb=" O ALA V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS V 103 " --> pdb=" O ASN V 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR V 138 " --> pdb=" O ILE V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS V 144 " --> pdb=" O ASN V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS V 173 " --> pdb=" O TYR V 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR V 175 " --> pdb=" O PHE V 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY V 177 " --> pdb=" O LYS V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 42 removed outlier: 3.810A pdb=" N ASN W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG W 23 " --> pdb=" O ALA W 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU W 36 " --> pdb=" O SER W 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER W 37 " --> pdb=" O TYR W 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA W 53 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS W 54 " --> pdb=" O LYS W 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS W 61 " --> pdb=" O LEU W 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU W 62 " --> pdb=" O HIS W 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET W 71 " --> pdb=" O ALA W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.587A pdb=" N CYS W 103 " --> pdb=" O ASN W 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 125 " --> pdb=" O LEU W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR W 138 " --> pdb=" O ILE W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS W 144 " --> pdb=" O ASN W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 177 removed outlier: 4.010A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 173 " --> pdb=" O TYR W 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR W 175 " --> pdb=" O PHE W 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY W 177 " --> pdb=" O LYS W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 42 removed outlier: 3.811A pdb=" N ASN X 22 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG X 23 " --> pdb=" O ALA X 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 36 " --> pdb=" O SER X 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER X 37 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 77 removed outlier: 3.997A pdb=" N ALA X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU X 62 " --> pdb=" O HIS X 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET X 71 " --> pdb=" O ALA X 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.588A pdb=" N CYS X 103 " --> pdb=" O ASN X 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 138 removed outlier: 3.817A pdb=" N TYR X 138 " --> pdb=" O ILE X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 160 removed outlier: 3.552A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS X 144 " --> pdb=" O ASN X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 177 removed outlier: 4.009A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS X 173 " --> pdb=" O TYR X 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR X 175 " --> pdb=" O PHE X 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY X 177 " --> pdb=" O LYS X 173 " (cutoff:3.500A) 2139 hydrogen bonds defined for protein. 6417 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: 9.58 Time building geometry restraints manager: 13.34 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: 11500 1.34 - 1.46: 6203 1.46 - 1.57: 16545 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 34512 Sorted by residual: bond pdb=" CG TYR H 40 " pdb=" CD2 TYR H 40 " ideal model delta sigma weight residual 1.389 1.362 0.027 2.10e-02 2.27e+03 1.63e+00 bond pdb=" CG TYR E 40 " pdb=" CD2 TYR E 40 " ideal model delta sigma weight residual 1.389 1.363 0.026 2.10e-02 2.27e+03 1.48e+00 bond pdb=" CG TYR B 40 " pdb=" CD2 TYR B 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.41e+00 bond pdb=" CG TYR W 40 " pdb=" CD2 TYR W 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.39e+00 bond pdb=" CG TYR O 40 " pdb=" CD2 TYR O 40 " ideal model delta sigma weight residual 1.389 1.364 0.025 2.10e-02 2.27e+03 1.38e+00 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 664 106.65 - 113.49: 19868 113.49 - 120.34: 13595 120.34 - 127.18: 11997 127.18 - 134.03: 364 Bond angle restraints: 46488 Sorted by residual: angle pdb=" N GLU P 95 " pdb=" CA GLU P 95 " pdb=" C GLU P 95 " ideal model delta sigma weight residual 110.80 115.71 -4.91 2.13e+00 2.20e-01 5.31e+00 angle pdb=" N GLU C 95 " pdb=" CA GLU C 95 " pdb=" C GLU C 95 " ideal model delta sigma weight residual 110.80 115.70 -4.90 2.13e+00 2.20e-01 5.29e+00 angle pdb=" N GLU M 95 " pdb=" CA GLU M 95 " pdb=" C GLU M 95 " ideal model delta sigma weight residual 110.80 115.70 -4.90 2.13e+00 2.20e-01 5.29e+00 angle pdb=" N GLU Q 95 " pdb=" CA GLU Q 95 " pdb=" C GLU Q 95 " ideal model delta sigma weight residual 110.80 115.69 -4.89 2.13e+00 2.20e-01 5.26e+00 angle pdb=" N GLU I 95 " pdb=" CA GLU I 95 " pdb=" C GLU I 95 " ideal model delta sigma weight residual 110.80 115.69 -4.89 2.13e+00 2.20e-01 5.26e+00 ... (remaining 46483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 20310 15.77 - 31.54: 282 31.54 - 47.31: 144 47.31 - 63.08: 24 63.08 - 78.85: 96 Dihedral angle restraints: 20856 sinusoidal: 8616 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP K 94 " pdb=" C TRP K 94 " pdb=" N GLU K 95 " pdb=" CA GLU K 95 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP N 94 " pdb=" C TRP N 94 " pdb=" N GLU N 95 " pdb=" CA GLU N 95 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1671 0.024 - 0.047: 1795 0.047 - 0.071: 1077 0.071 - 0.094: 230 0.094 - 0.118: 123 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA HIS H 174 " pdb=" N HIS H 174 " pdb=" C HIS H 174 " pdb=" CB HIS H 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA HIS W 174 " pdb=" N HIS W 174 " pdb=" C HIS W 174 " pdb=" CB HIS W 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA HIS C 174 " pdb=" N HIS C 174 " pdb=" C HIS C 174 " pdb=" CB HIS C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 4893 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE X 82 " -0.050 2.00e-02 2.50e+03 4.46e-02 3.48e+01 pdb=" CG PHE X 82 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE X 82 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE X 82 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE X 82 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE X 82 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE X 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 82 " 0.051 2.00e-02 2.50e+03 4.40e-02 3.38e+01 pdb=" CG PHE J 82 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE J 82 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE J 82 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE J 82 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE J 82 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE J 82 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 82 " 0.048 2.00e-02 2.50e+03 4.26e-02 3.18e+01 pdb=" CG PHE L 82 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE L 82 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE L 82 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE L 82 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE L 82 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE L 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10985 2.83 - 3.35: 34886 3.35 - 3.87: 52450 3.87 - 4.38: 61299 4.38 - 4.90: 101032 Nonbonded interactions: 260652 Sorted by model distance: nonbonded pdb=" OD1 ASP J 85 " pdb=" N LYS V 88 " model vdw 2.314 2.520 nonbonded pdb=" O GLY B 79 " pdb=" NH1 ARG B 80 " model vdw 2.326 2.520 nonbonded pdb=" O GLY K 79 " pdb=" NH1 ARG K 80 " model vdw 2.326 2.520 nonbonded pdb=" O GLY D 79 " pdb=" NH1 ARG D 80 " model vdw 2.327 2.520 nonbonded pdb=" O GLY S 79 " pdb=" NH1 ARG S 80 " model vdw 2.327 2.520 ... (remaining 260647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.120 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: 2.590 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 80.800 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.300 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.007 0.033 34512 Z= 0.458 Angle : 0.682 6.913 46488 Z= 0.364 Chirality : 0.043 0.118 4896 Planarity : 0.004 0.045 6120 Dihedral : 10.513 78.853 12936 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -4.00 (0.10), residues: 4080 helix: -2.91 (0.06), residues: 3000 sheet: None (None), residues: 0 loop : -1.03 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 94 HIS 0.004 0.001 HIS A 58 PHE 0.103 0.005 PHE X 82 TYR 0.013 0.002 TYR G 40 ARG 0.004 0.001 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1845 time to evaluate : 6.577 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: A 16 ASP cc_start: 0.7608 (m-30) cc_final: 0.7273 (t0) REVERT: A 64 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8097 (ttp-170) REVERT: B 45 ASP cc_start: 0.8239 (p0) cc_final: 0.7889 (t0) REVERT: B 95 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7503 (tt0) REVERT: C 18 GLU cc_start: 0.8447 (tt0) cc_final: 0.7615 (tm-30) REVERT: C 68 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8535 (tm-30) REVERT: C 86 ILE cc_start: 0.9135 (mt) cc_final: 0.8329 (tt) REVERT: C 90 ASP cc_start: 0.8185 (m-30) cc_final: 0.7916 (p0) REVERT: C 127 ASP cc_start: 0.8155 (t0) cc_final: 0.7844 (t0) REVERT: C 173 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8242 (tptp) REVERT: D 16 ASP cc_start: 0.7696 (m-30) cc_final: 0.7433 (t0) REVERT: D 43 ASP cc_start: 0.9099 (t70) cc_final: 0.8896 (t0) REVERT: D 46 ASP cc_start: 0.9126 (p0) cc_final: 0.8818 (m-30) REVERT: D 86 ILE cc_start: 0.7937 (mt) cc_final: 0.7553 (pt) REVERT: D 87 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7672 (mttt) REVERT: D 127 ASP cc_start: 0.7181 (t0) cc_final: 0.6324 (p0) REVERT: D 154 THR cc_start: 0.8984 (m) cc_final: 0.8725 (p) REVERT: E 14 HIS cc_start: 0.6776 (t-90) cc_final: 0.6536 (t70) REVERT: E 16 ASP cc_start: 0.8609 (m-30) cc_final: 0.8269 (t0) REVERT: E 18 GLU cc_start: 0.9193 (tt0) cc_final: 0.8816 (pt0) REVERT: E 24 GLN cc_start: 0.8748 (tp40) cc_final: 0.8512 (tm-30) REVERT: E 45 ASP cc_start: 0.7452 (p0) cc_final: 0.7047 (t70) REVERT: E 175 THR cc_start: 0.8179 (m) cc_final: 0.7808 (p) REVERT: F 85 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: F 86 ILE cc_start: 0.7985 (mt) cc_final: 0.7525 (tp) REVERT: F 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.8014 (p0) REVERT: F 99 ASN cc_start: 0.9014 (t0) cc_final: 0.8789 (t0) REVERT: F 101 MET cc_start: 0.9098 (mmt) cc_final: 0.8897 (mmt) REVERT: F 117 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8204 (tp30) REVERT: F 127 ASP cc_start: 0.7823 (t0) cc_final: 0.7544 (t0) REVERT: G 45 ASP cc_start: 0.7428 (p0) cc_final: 0.7177 (t0) REVERT: G 85 ASP cc_start: 0.8152 (m-30) cc_final: 0.6900 (p0) REVERT: G 86 ILE cc_start: 0.8648 (mt) cc_final: 0.8404 (mp) REVERT: G 109 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8850 (mtpt) REVERT: G 123 THR cc_start: 0.8501 (m) cc_final: 0.8178 (p) REVERT: H 46 ASP cc_start: 0.8121 (p0) cc_final: 0.7726 (t0) REVERT: H 86 ILE cc_start: 0.8154 (mt) cc_final: 0.7860 (tp) REVERT: H 93 ASP cc_start: 0.8621 (t0) cc_final: 0.8394 (p0) REVERT: H 95 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8072 (tm-30) REVERT: H 127 ASP cc_start: 0.8477 (t0) cc_final: 0.8127 (t0) REVERT: I 18 GLU cc_start: 0.8607 (tt0) cc_final: 0.8316 (tm-30) REVERT: I 90 ASP cc_start: 0.8278 (m-30) cc_final: 0.7767 (p0) REVERT: I 95 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8223 (tm-30) REVERT: I 127 ASP cc_start: 0.8607 (t0) cc_final: 0.8291 (OUTLIER) REVERT: I 159 MET cc_start: 0.7905 (mtp) cc_final: 0.6843 (ttm) REVERT: I 175 THR cc_start: 0.7636 (m) cc_final: 0.7170 (p) REVERT: J 24 GLN cc_start: 0.9072 (tp40) cc_final: 0.8754 (tm-30) REVERT: J 64 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7980 (ttp-170) REVERT: J 102 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7637 (tm-30) REVERT: J 113 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8283 (tm-30) REVERT: K 12 ASN cc_start: 0.8727 (t0) cc_final: 0.8424 (t0) REVERT: K 68 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8417 (tm-30) REVERT: K 76 GLN cc_start: 0.9371 (mt0) cc_final: 0.9111 (mp10) REVERT: K 115 LEU cc_start: 0.7998 (mt) cc_final: 0.7696 (tm) REVERT: K 117 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7826 (pp20) REVERT: K 126 ASN cc_start: 0.7672 (m-40) cc_final: 0.7245 (p0) REVERT: K 168 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8804 (mt-10) REVERT: L 23 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7125 (tpp80) REVERT: L 84 GLN cc_start: 0.7769 (mm110) cc_final: 0.7501 (mm-40) REVERT: L 90 ASP cc_start: 0.7974 (m-30) cc_final: 0.7626 (p0) REVERT: L 91 CYS cc_start: 0.7657 (m) cc_final: 0.7325 (t) REVERT: L 92 ASP cc_start: 0.8777 (m-30) cc_final: 0.8525 (t0) REVERT: L 102 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7930 (pp20) REVERT: M 68 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8878 (tp30) REVERT: M 108 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7927 (tm-30) REVERT: N 12 ASN cc_start: 0.8767 (t0) cc_final: 0.8198 (t0) REVERT: N 14 HIS cc_start: 0.6405 (t-90) cc_final: 0.6189 (t-90) REVERT: N 45 ASP cc_start: 0.8263 (p0) cc_final: 0.7459 (t70) REVERT: N 62 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7437 (tm-30) REVERT: N 82 PHE cc_start: 0.8132 (m-80) cc_final: 0.7871 (m-80) REVERT: N 84 GLN cc_start: 0.8327 (mm110) cc_final: 0.8015 (mm-40) REVERT: N 92 ASP cc_start: 0.6276 (m-30) cc_final: 0.6016 (m-30) REVERT: P 22 ASN cc_start: 0.8766 (m-40) cc_final: 0.8561 (m110) REVERT: P 45 ASP cc_start: 0.8064 (p0) cc_final: 0.7543 (t70) REVERT: P 68 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8644 (mt-10) REVERT: P 87 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7801 (ttpt) REVERT: Q 18 GLU cc_start: 0.8903 (tt0) cc_final: 0.8650 (tp30) REVERT: Q 34 VAL cc_start: 0.7859 (t) cc_final: 0.7370 (t) REVERT: Q 55 TYR cc_start: 0.8380 (t80) cc_final: 0.8178 (t80) REVERT: Q 85 ASP cc_start: 0.8905 (m-30) cc_final: 0.8443 (p0) REVERT: Q 88 LYS cc_start: 0.8381 (pttp) cc_final: 0.8122 (ptpp) REVERT: Q 95 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7426 (tp30) REVERT: Q 138 TYR cc_start: 0.8240 (m-80) cc_final: 0.8008 (m-80) REVERT: Q 140 ASN cc_start: 0.8873 (t0) cc_final: 0.8660 (t0) REVERT: Q 158 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8979 (ttmm) REVERT: R 11 GLN cc_start: 0.8121 (tt0) cc_final: 0.7481 (tm130) REVERT: R 64 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7754 (ttt90) REVERT: R 85 ASP cc_start: 0.7662 (m-30) cc_final: 0.7350 (m-30) REVERT: R 92 ASP cc_start: 0.8030 (m-30) cc_final: 0.7659 (p0) REVERT: R 138 TYR cc_start: 0.8406 (m-80) cc_final: 0.8189 (m-80) REVERT: R 169 TYR cc_start: 0.8460 (t80) cc_final: 0.8083 (t80) REVERT: S 55 TYR cc_start: 0.8571 (t80) cc_final: 0.7573 (t80) REVERT: S 58 HIS cc_start: 0.7535 (t70) cc_final: 0.7276 (t70) REVERT: S 68 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8792 (mt-10) REVERT: S 87 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6436 (pttp) REVERT: S 88 LYS cc_start: 0.8007 (pttp) cc_final: 0.7784 (pttm) REVERT: T 11 GLN cc_start: 0.8555 (tt0) cc_final: 0.8331 (tt0) REVERT: T 12 ASN cc_start: 0.7875 (t0) cc_final: 0.7649 (t0) REVERT: T 92 ASP cc_start: 0.7554 (m-30) cc_final: 0.6961 (p0) REVERT: T 102 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8718 (tm-30) REVERT: U 14 HIS cc_start: 0.7827 (t-90) cc_final: 0.7592 (t-90) REVERT: U 18 GLU cc_start: 0.8199 (tt0) cc_final: 0.7953 (tm-30) REVERT: U 47 VAL cc_start: 0.8096 (t) cc_final: 0.7815 (m) REVERT: U 54 LYS cc_start: 0.8570 (mttt) cc_final: 0.8328 (mtmp) REVERT: U 85 ASP cc_start: 0.8475 (m-30) cc_final: 0.8167 (m-30) REVERT: V 18 GLU cc_start: 0.8791 (tt0) cc_final: 0.8565 (tp30) REVERT: V 24 GLN cc_start: 0.8965 (tp40) cc_final: 0.8693 (tp40) REVERT: V 72 LYS cc_start: 0.8330 (tttt) cc_final: 0.7965 (ttpp) REVERT: V 80 ARG cc_start: 0.7001 (mmt-90) cc_final: 0.6610 (mpt-90) REVERT: V 88 LYS cc_start: 0.8839 (pttp) cc_final: 0.8285 (pmtt) REVERT: V 117 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8125 (mp0) REVERT: V 164 SER cc_start: 0.7087 (t) cc_final: 0.6254 (m) REVERT: W 68 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8774 (tt0) REVERT: W 90 ASP cc_start: 0.8141 (m-30) cc_final: 0.7391 (t0) REVERT: W 92 ASP cc_start: 0.6660 (m-30) cc_final: 0.6307 (p0) REVERT: W 99 ASN cc_start: 0.8941 (t0) cc_final: 0.8720 (t0) REVERT: X 13 TYR cc_start: 0.6374 (t80) cc_final: 0.6021 (t80) REVERT: X 80 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7088 (pmm150) REVERT: X 85 ASP cc_start: 0.7885 (m-30) cc_final: 0.7139 (p0) REVERT: X 94 TRP cc_start: 0.7928 (m100) cc_final: 0.7629 (m100) REVERT: X 95 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7737 (tm-30) outliers start: 0 outliers final: 9 residues processed: 1845 average time/residue: 1.5527 time to fit residues: 3365.7866 Evaluate side-chains 691 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 683 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain V residue 41 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 0.0270 chunk 370 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS A 140 ASN A 152 HIS B 14 HIS B 26 ASN B 51 ASN C 12 ASN C 22 ASN C 126 ASN D 76 GLN D 155 ASN E 61 HIS E 126 ASN F 22 ASN ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 66 HIS ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN H 22 ASN H 24 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN I 140 ASN J 126 ASN J 137 HIS J 155 ASN K 22 ASN K 51 ASN K 59 GLN K 137 HIS K 155 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN N 22 ASN N 24 GLN O 22 ASN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 ASN O 155 ASN P 113 GLN P 126 ASN Q 99 ASN R 12 ASN R 14 HIS R 26 ASN R 61 HIS R 155 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 GLN T 75 ASN U 61 HIS ** U 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS V 59 GLN V 113 GLN ** V 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN ** W 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.223 Angle : 0.683 8.796 46488 Z= 0.355 Chirality : 0.039 0.187 4896 Planarity : 0.004 0.082 6120 Dihedral : 4.666 51.368 4504 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.25 % Allowed : 22.34 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 4080 helix: 0.77 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -0.89 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 94 HIS 0.012 0.001 HIS A 106 PHE 0.016 0.001 PHE R 171 TYR 0.025 0.002 TYR R 138 ARG 0.009 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 960 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8617 (ttt90) cc_final: 0.8372 (ttp-170) REVERT: A 124 ASP cc_start: 0.8395 (m-30) cc_final: 0.8147 (m-30) REVERT: B 24 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 58 HIS cc_start: 0.7235 (t70) cc_final: 0.6921 (t70) REVERT: B 76 GLN cc_start: 0.8190 (mt0) cc_final: 0.7904 (mt0) REVERT: C 45 ASP cc_start: 0.8014 (p0) cc_final: 0.6807 (t0) REVERT: C 86 ILE cc_start: 0.9123 (mt) cc_final: 0.8387 (tt) REVERT: C 90 ASP cc_start: 0.8331 (m-30) cc_final: 0.7990 (p0) REVERT: C 124 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6161 (p0) REVERT: C 127 ASP cc_start: 0.7604 (t0) cc_final: 0.7388 (t0) REVERT: D 16 ASP cc_start: 0.7526 (m-30) cc_final: 0.6987 (t0) REVERT: D 43 ASP cc_start: 0.9340 (t70) cc_final: 0.8944 (t0) REVERT: D 46 ASP cc_start: 0.9143 (p0) cc_final: 0.8734 (m-30) REVERT: D 62 GLU cc_start: 0.7419 (mp0) cc_final: 0.7082 (mm-30) REVERT: D 127 ASP cc_start: 0.6667 (t0) cc_final: 0.5959 (p0) REVERT: D 140 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (m-40) REVERT: E 18 GLU cc_start: 0.9255 (tt0) cc_final: 0.8948 (tt0) REVERT: E 24 GLN cc_start: 0.8342 (tp40) cc_final: 0.8103 (tm-30) REVERT: E 45 ASP cc_start: 0.6914 (p0) cc_final: 0.6644 (t70) REVERT: E 71 MET cc_start: 0.8735 (tpp) cc_final: 0.8157 (pp-130) REVERT: E 92 ASP cc_start: 0.8554 (m-30) cc_final: 0.7795 (t0) REVERT: E 142 GLN cc_start: 0.8338 (mm110) cc_final: 0.8134 (mm-40) REVERT: E 157 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7744 (ttp-110) REVERT: E 175 THR cc_start: 0.7712 (m) cc_final: 0.7366 (p) REVERT: F 11 GLN cc_start: 0.7296 (tm-30) cc_final: 0.7052 (tm-30) REVERT: F 38 MET cc_start: 0.8012 (mtp) cc_final: 0.7724 (ttm) REVERT: F 47 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8980 (m) REVERT: F 85 ASP cc_start: 0.8211 (m-30) cc_final: 0.7901 (m-30) REVERT: F 90 ASP cc_start: 0.8372 (m-30) cc_final: 0.8084 (p0) REVERT: F 117 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8282 (tp30) REVERT: F 132 ASP cc_start: 0.8166 (t70) cc_final: 0.7964 (t70) REVERT: G 85 ASP cc_start: 0.8187 (m-30) cc_final: 0.6860 (p0) REVERT: G 86 ILE cc_start: 0.8679 (mt) cc_final: 0.8478 (mp) REVERT: G 90 ASP cc_start: 0.5702 (OUTLIER) cc_final: 0.5469 (p0) REVERT: H 46 ASP cc_start: 0.8276 (p0) cc_final: 0.7568 (t0) REVERT: H 86 ILE cc_start: 0.8158 (mt) cc_final: 0.7923 (tp) REVERT: H 93 ASP cc_start: 0.8604 (t0) cc_final: 0.8060 (p0) REVERT: H 96 SER cc_start: 0.6702 (m) cc_final: 0.6321 (p) REVERT: H 127 ASP cc_start: 0.8374 (t0) cc_final: 0.7983 (t0) REVERT: I 18 GLU cc_start: 0.8606 (tt0) cc_final: 0.8403 (tp30) REVERT: I 74 GLN cc_start: 0.8763 (tp40) cc_final: 0.7856 (tp-100) REVERT: I 90 ASP cc_start: 0.8362 (m-30) cc_final: 0.7700 (t0) REVERT: I 95 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8363 (tm-30) REVERT: I 126 ASN cc_start: 0.7750 (m-40) cc_final: 0.7518 (p0) REVERT: J 24 GLN cc_start: 0.8970 (tp40) cc_final: 0.8563 (tm-30) REVERT: J 64 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8258 (ttt90) REVERT: J 71 MET cc_start: 0.9055 (mtm) cc_final: 0.8709 (ttm) REVERT: J 102 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7624 (tm-30) REVERT: J 113 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8236 (tm-30) REVERT: K 40 TYR cc_start: 0.8477 (m-80) cc_final: 0.7974 (m-80) REVERT: K 51 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7925 (t0) REVERT: L 84 GLN cc_start: 0.7772 (mm110) cc_final: 0.7503 (mm-40) REVERT: L 90 ASP cc_start: 0.7697 (m-30) cc_final: 0.7086 (p0) REVERT: L 91 CYS cc_start: 0.7455 (m) cc_final: 0.6443 (m) REVERT: L 92 ASP cc_start: 0.8899 (m-30) cc_final: 0.8353 (t0) REVERT: L 102 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7818 (pp20) REVERT: M 40 TYR cc_start: 0.8638 (m-10) cc_final: 0.8387 (m-10) REVERT: M 70 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8035 (mm) REVERT: M 84 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7335 (mm110) REVERT: M 108 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7375 (tm-30) REVERT: N 45 ASP cc_start: 0.8210 (p0) cc_final: 0.7630 (t70) REVERT: N 84 GLN cc_start: 0.8457 (mm110) cc_final: 0.7911 (mm-40) REVERT: N 102 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7741 (tm-30) REVERT: O 7 SER cc_start: 0.8427 (m) cc_final: 0.8080 (p) REVERT: O 101 MET cc_start: 0.9018 (tpp) cc_final: 0.8741 (mpp) REVERT: P 45 ASP cc_start: 0.8145 (p0) cc_final: 0.7385 (t70) REVERT: P 65 GLU cc_start: 0.8741 (tp30) cc_final: 0.8453 (tp30) REVERT: P 68 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8652 (pp20) REVERT: P 76 GLN cc_start: 0.9172 (mt0) cc_final: 0.8875 (mp10) REVERT: P 77 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8155 (mmm160) REVERT: Q 18 GLU cc_start: 0.9083 (tt0) cc_final: 0.8792 (tp30) REVERT: Q 80 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8049 (mmm160) REVERT: Q 85 ASP cc_start: 0.8982 (m-30) cc_final: 0.8527 (p0) REVERT: R 11 GLN cc_start: 0.8130 (tt0) cc_final: 0.7439 (tp-100) REVERT: R 92 ASP cc_start: 0.8133 (m-30) cc_final: 0.7671 (t0) REVERT: R 154 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8405 (t) REVERT: S 58 HIS cc_start: 0.7211 (t70) cc_final: 0.7009 (t-90) REVERT: S 68 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8739 (mt-10) REVERT: S 87 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6367 (pttm) REVERT: S 151 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8076 (t0) REVERT: S 169 TYR cc_start: 0.7201 (t80) cc_final: 0.6993 (t80) REVERT: T 32 SER cc_start: 0.8284 (m) cc_final: 0.8080 (t) REVERT: T 92 ASP cc_start: 0.7827 (m-30) cc_final: 0.7118 (p0) REVERT: T 102 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8802 (tm-30) REVERT: V 18 GLU cc_start: 0.8800 (tt0) cc_final: 0.8564 (tp30) REVERT: V 72 LYS cc_start: 0.8441 (tttt) cc_final: 0.8164 (ttpp) REVERT: V 74 GLN cc_start: 0.8349 (tp-100) cc_final: 0.7948 (tp-100) REVERT: W 68 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8752 (tt0) REVERT: W 74 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8120 (tp-100) REVERT: W 80 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8694 (mpt180) REVERT: W 90 ASP cc_start: 0.8151 (m-30) cc_final: 0.7847 (m-30) REVERT: W 92 ASP cc_start: 0.6656 (m-30) cc_final: 0.6294 (p0) REVERT: X 13 TYR cc_start: 0.6421 (t80) cc_final: 0.5928 (t80) outliers start: 228 outliers final: 46 residues processed: 1102 average time/residue: 1.3139 time to fit residues: 1744.2390 Evaluate side-chains 706 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 651 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 151 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain X residue 64 ARG Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 297 optimal weight: 30.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS B 26 ASN C 126 ASN F 66 HIS F 113 GLN ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN H 113 GLN H 137 HIS ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN J 74 GLN K 24 GLN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN M 137 HIS ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN O 22 ASN O 24 GLN O 26 ASN O 76 GLN O 152 HIS P 74 GLN P 106 HIS P 126 ASN R 14 HIS R 24 GLN ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 12 ASN S 24 GLN S 75 ASN S 76 GLN ** S 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 ASN U 119 HIS ** U 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 GLN ** V 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 HIS W 110 ASN ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 119 HIS X 24 GLN X 84 GLN ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34512 Z= 0.217 Angle : 0.635 10.511 46488 Z= 0.330 Chirality : 0.040 0.184 4896 Planarity : 0.004 0.067 6120 Dihedral : 4.320 23.634 4492 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.50 % Allowed : 25.93 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 1.95 (0.12), residues: 4080 helix: 1.87 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.66 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 94 HIS 0.014 0.001 HIS A 106 PHE 0.010 0.001 PHE D 133 TYR 0.037 0.002 TYR K 169 ARG 0.011 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 734 time to evaluate : 3.903 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: A 12 ASN cc_start: 0.9358 (t0) cc_final: 0.8917 (t0) REVERT: A 64 ARG cc_start: 0.8776 (ttt90) cc_final: 0.8556 (ttp-170) REVERT: A 164 SER cc_start: 0.7584 (t) cc_final: 0.7141 (p) REVERT: B 24 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 58 HIS cc_start: 0.7197 (t70) cc_final: 0.6933 (t70) REVERT: B 109 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8744 (tppp) REVERT: C 45 ASP cc_start: 0.8152 (p0) cc_final: 0.6949 (t0) REVERT: C 68 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8146 (tm-30) REVERT: C 90 ASP cc_start: 0.8223 (m-30) cc_final: 0.7877 (p0) REVERT: C 124 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5825 (p0) REVERT: C 127 ASP cc_start: 0.7897 (t0) cc_final: 0.7641 (t0) REVERT: D 16 ASP cc_start: 0.7478 (m-30) cc_final: 0.6998 (t0) REVERT: D 43 ASP cc_start: 0.9306 (t70) cc_final: 0.8922 (t0) REVERT: D 46 ASP cc_start: 0.8946 (p0) cc_final: 0.8676 (m-30) REVERT: D 62 GLU cc_start: 0.7700 (mp0) cc_final: 0.7417 (mm-30) REVERT: D 75 ASN cc_start: 0.8251 (m-40) cc_final: 0.7888 (t0) REVERT: D 127 ASP cc_start: 0.6625 (t0) cc_final: 0.5729 (p0) REVERT: E 11 GLN cc_start: 0.8847 (tt0) cc_final: 0.8409 (tm130) REVERT: E 24 GLN cc_start: 0.8182 (tp40) cc_final: 0.7958 (tm-30) REVERT: E 45 ASP cc_start: 0.6664 (p0) cc_final: 0.6149 (t70) REVERT: E 85 ASP cc_start: 0.7890 (m-30) cc_final: 0.7221 (p0) REVERT: E 86 ILE cc_start: 0.8175 (mp) cc_final: 0.7886 (OUTLIER) REVERT: E 92 ASP cc_start: 0.8719 (m-30) cc_final: 0.7957 (t0) REVERT: E 142 GLN cc_start: 0.8517 (mm110) cc_final: 0.8280 (mm-40) REVERT: E 157 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7765 (ttp-110) REVERT: E 175 THR cc_start: 0.7778 (m) cc_final: 0.7472 (p) REVERT: F 11 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7265 (tm-30) REVERT: F 38 MET cc_start: 0.8052 (mtp) cc_final: 0.7808 (ttm) REVERT: F 47 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (m) REVERT: F 85 ASP cc_start: 0.8109 (m-30) cc_final: 0.7856 (m-30) REVERT: F 90 ASP cc_start: 0.8465 (m-30) cc_final: 0.8183 (p0) REVERT: F 117 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8243 (tp30) REVERT: G 16 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7330 (t0) REVERT: G 45 ASP cc_start: 0.6455 (t0) cc_final: 0.6033 (t0) REVERT: G 106 HIS cc_start: 0.7451 (t70) cc_final: 0.6733 (m-70) REVERT: H 46 ASP cc_start: 0.8409 (p0) cc_final: 0.7681 (t0) REVERT: H 65 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (mm-30) REVERT: H 86 ILE cc_start: 0.8179 (mt) cc_final: 0.7671 (tp) REVERT: H 127 ASP cc_start: 0.8491 (t0) cc_final: 0.8036 (t0) REVERT: I 74 GLN cc_start: 0.8734 (tp40) cc_final: 0.8384 (tm-30) REVERT: I 90 ASP cc_start: 0.8428 (m-30) cc_final: 0.7714 (t0) REVERT: I 95 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8450 (tm-30) REVERT: J 24 GLN cc_start: 0.9029 (tp40) cc_final: 0.8497 (tm-30) REVERT: J 64 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8526 (ttp80) REVERT: J 71 MET cc_start: 0.9089 (mtm) cc_final: 0.8880 (ttm) REVERT: J 76 GLN cc_start: 0.8607 (mt0) cc_final: 0.8380 (mt0) REVERT: J 102 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7674 (tm-30) REVERT: J 113 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8331 (tm-30) REVERT: K 51 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: L 11 GLN cc_start: 0.8057 (tt0) cc_final: 0.7731 (tm-30) REVERT: L 24 GLN cc_start: 0.8315 (tp40) cc_final: 0.7986 (tm-30) REVERT: L 84 GLN cc_start: 0.7746 (mm110) cc_final: 0.7466 (mm-40) REVERT: L 90 ASP cc_start: 0.7804 (m-30) cc_final: 0.7105 (p0) REVERT: L 92 ASP cc_start: 0.8998 (m-30) cc_final: 0.8444 (t0) REVERT: L 102 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7783 (pp20) REVERT: L 113 GLN cc_start: 0.8892 (tt0) cc_final: 0.8676 (pt0) REVERT: M 70 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7878 (mm) REVERT: M 84 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7528 (mm110) REVERT: M 108 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7374 (tm-30) REVERT: N 102 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7651 (tm-30) REVERT: O 7 SER cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (p) REVERT: P 43 ASP cc_start: 0.8374 (t0) cc_final: 0.8085 (t0) REVERT: P 51 ASN cc_start: 0.8360 (m110) cc_final: 0.8137 (m110) REVERT: P 65 GLU cc_start: 0.8799 (tp30) cc_final: 0.8545 (tp30) REVERT: P 68 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8592 (pp20) REVERT: P 76 GLN cc_start: 0.9172 (mt0) cc_final: 0.8865 (mp10) REVERT: Q 18 GLU cc_start: 0.9103 (tt0) cc_final: 0.8799 (tp30) REVERT: Q 32 SER cc_start: 0.8560 (t) cc_final: 0.8231 (m) REVERT: Q 43 ASP cc_start: 0.8392 (t0) cc_final: 0.8161 (t0) REVERT: R 8 GLN cc_start: 0.8543 (pt0) cc_final: 0.8313 (pm20) REVERT: R 11 GLN cc_start: 0.8383 (tt0) cc_final: 0.7711 (tp-100) REVERT: R 92 ASP cc_start: 0.8193 (m-30) cc_final: 0.7695 (t0) REVERT: R 154 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8336 (t) REVERT: R 159 MET cc_start: 0.8402 (mtp) cc_final: 0.7938 (ttm) REVERT: S 24 GLN cc_start: 0.7196 (tp-100) cc_final: 0.6733 (tm-30) REVERT: S 68 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8728 (mt-10) REVERT: S 87 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6729 (pttp) REVERT: T 92 ASP cc_start: 0.7804 (m-30) cc_final: 0.7036 (p0) REVERT: T 102 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8752 (tm-30) REVERT: U 18 GLU cc_start: 0.8139 (tp30) cc_final: 0.7703 (tm-30) REVERT: U 86 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7844 (tp) REVERT: V 18 GLU cc_start: 0.8743 (tt0) cc_final: 0.8486 (tp30) REVERT: V 35 TYR cc_start: 0.8660 (m-80) cc_final: 0.8322 (m-10) REVERT: V 72 LYS cc_start: 0.8577 (tttt) cc_final: 0.8261 (ttpp) REVERT: V 74 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8238 (tm-30) REVERT: V 85 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: W 11 GLN cc_start: 0.8338 (tp40) cc_final: 0.7865 (pm20) REVERT: W 68 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8814 (tt0) REVERT: W 74 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8342 (tp-100) REVERT: W 80 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8767 (mpt180) REVERT: W 90 ASP cc_start: 0.8443 (m-30) cc_final: 0.8062 (m-30) REVERT: W 92 ASP cc_start: 0.6672 (m-30) cc_final: 0.6232 (p0) REVERT: X 13 TYR cc_start: 0.6463 (t80) cc_final: 0.5950 (t80) REVERT: X 70 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8427 (mm) outliers start: 237 outliers final: 77 residues processed: 903 average time/residue: 1.3445 time to fit residues: 1465.9605 Evaluate side-chains 704 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 615 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 22 ASN Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 170 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 22 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS B 26 ASN B 74 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN D 74 GLN E 75 ASN E 76 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN I 76 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN K 74 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN O 22 ASN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS P 126 ASN Q 112 ASN R 14 HIS ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN V 59 GLN ** V 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 HIS ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 66 HIS ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34512 Z= 0.248 Angle : 0.638 10.476 46488 Z= 0.334 Chirality : 0.040 0.231 4896 Planarity : 0.004 0.077 6120 Dihedral : 4.312 23.332 4488 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 6.99 % Allowed : 27.52 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.30 (0.13), residues: 4080 helix: 2.21 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.82 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.013 0.001 HIS P 106 PHE 0.027 0.001 PHE R 133 TYR 0.027 0.002 TYR Q 169 ARG 0.015 0.001 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 672 time to evaluate : 4.266 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: A 12 ASN cc_start: 0.9459 (t0) cc_final: 0.8880 (t0) REVERT: A 24 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 64 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8590 (ttp-170) REVERT: B 24 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 58 HIS cc_start: 0.7165 (t70) cc_final: 0.6886 (t70) REVERT: C 13 TYR cc_start: 0.7945 (t80) cc_final: 0.7589 (t80) REVERT: C 45 ASP cc_start: 0.8350 (p0) cc_final: 0.7382 (t0) REVERT: C 86 ILE cc_start: 0.8937 (mt) cc_final: 0.8385 (tt) REVERT: C 90 ASP cc_start: 0.8329 (m-30) cc_final: 0.7916 (p0) REVERT: C 124 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.5813 (p0) REVERT: C 127 ASP cc_start: 0.8105 (t0) cc_final: 0.7780 (t0) REVERT: C 138 TYR cc_start: 0.8764 (m-10) cc_final: 0.8540 (m-10) REVERT: C 159 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: D 16 ASP cc_start: 0.7483 (m-30) cc_final: 0.6980 (t0) REVERT: D 43 ASP cc_start: 0.9459 (t70) cc_final: 0.9114 (t0) REVERT: D 62 GLU cc_start: 0.7722 (mp0) cc_final: 0.7449 (mm-30) REVERT: D 75 ASN cc_start: 0.8248 (m-40) cc_final: 0.7905 (t0) REVERT: D 127 ASP cc_start: 0.7196 (t0) cc_final: 0.6320 (p0) REVERT: E 11 GLN cc_start: 0.8827 (tt0) cc_final: 0.8385 (tm130) REVERT: E 24 GLN cc_start: 0.8043 (tp40) cc_final: 0.7842 (tm-30) REVERT: E 45 ASP cc_start: 0.6874 (p0) cc_final: 0.6173 (t0) REVERT: E 85 ASP cc_start: 0.7827 (m-30) cc_final: 0.7238 (p0) REVERT: E 92 ASP cc_start: 0.8736 (m-30) cc_final: 0.8031 (t0) REVERT: E 175 THR cc_start: 0.7776 (m) cc_final: 0.7494 (p) REVERT: F 38 MET cc_start: 0.8081 (mtp) cc_final: 0.7857 (ttm) REVERT: F 45 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7173 (p0) REVERT: F 47 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8909 (m) REVERT: F 85 ASP cc_start: 0.8071 (m-30) cc_final: 0.7795 (m-30) REVERT: F 90 ASP cc_start: 0.8532 (m-30) cc_final: 0.8201 (p0) REVERT: F 92 ASP cc_start: 0.8367 (m-30) cc_final: 0.7435 (t0) REVERT: F 106 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7150 (t70) REVERT: F 117 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8274 (tp30) REVERT: G 59 GLN cc_start: 0.8865 (tp40) cc_final: 0.8603 (tp40) REVERT: G 106 HIS cc_start: 0.7392 (t70) cc_final: 0.6779 (m-70) REVERT: H 46 ASP cc_start: 0.8409 (p0) cc_final: 0.7774 (t0) REVERT: H 65 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9028 (mm-30) REVERT: H 86 ILE cc_start: 0.8040 (mt) cc_final: 0.7735 (tp) REVERT: I 74 GLN cc_start: 0.8639 (tp40) cc_final: 0.8346 (tm-30) REVERT: I 90 ASP cc_start: 0.8297 (m-30) cc_final: 0.7501 (t0) REVERT: I 95 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8460 (tm-30) REVERT: J 24 GLN cc_start: 0.9077 (tp40) cc_final: 0.8548 (tm-30) REVERT: J 68 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8462 (tm-30) REVERT: J 71 MET cc_start: 0.9122 (mtm) cc_final: 0.8910 (ttm) REVERT: J 76 GLN cc_start: 0.8676 (mt0) cc_final: 0.8310 (mp10) REVERT: J 102 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7783 (tm-30) REVERT: K 51 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8008 (t0) REVERT: L 12 ASN cc_start: 0.7926 (t0) cc_final: 0.7285 (t0) REVERT: L 24 GLN cc_start: 0.8388 (tp40) cc_final: 0.8025 (tm-30) REVERT: L 75 ASN cc_start: 0.9098 (t0) cc_final: 0.8860 (t0) REVERT: L 84 GLN cc_start: 0.7805 (mm110) cc_final: 0.7507 (mm-40) REVERT: L 90 ASP cc_start: 0.7798 (m-30) cc_final: 0.6937 (p0) REVERT: L 92 ASP cc_start: 0.9154 (m-30) cc_final: 0.8442 (t0) REVERT: L 102 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7792 (pp20) REVERT: L 113 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8669 (pt0) REVERT: L 134 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8470 (tp) REVERT: M 81 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7729 (pp) REVERT: M 84 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7582 (mm110) REVERT: M 108 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7522 (tm-30) REVERT: N 86 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7838 (mm) REVERT: N 132 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6080 (m-30) REVERT: O 7 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7973 (p) REVERT: O 96 SER cc_start: 0.7604 (m) cc_final: 0.7320 (m) REVERT: O 169 TYR cc_start: 0.8462 (t80) cc_final: 0.8234 (t80) REVERT: P 43 ASP cc_start: 0.8466 (t70) cc_final: 0.8090 (t0) REVERT: P 51 ASN cc_start: 0.8430 (m110) cc_final: 0.8210 (m110) REVERT: P 64 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8059 (ttt-90) REVERT: P 76 GLN cc_start: 0.9146 (mt0) cc_final: 0.8808 (mp10) REVERT: P 159 MET cc_start: 0.8193 (ttp) cc_final: 0.7939 (ttp) REVERT: Q 18 GLU cc_start: 0.9114 (tt0) cc_final: 0.8796 (tp30) REVERT: Q 24 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8509 (tp-100) REVERT: Q 35 TYR cc_start: 0.8065 (m-10) cc_final: 0.7727 (m-80) REVERT: Q 169 TYR cc_start: 0.8860 (t80) cc_final: 0.8514 (t80) REVERT: R 8 GLN cc_start: 0.8572 (pt0) cc_final: 0.8310 (pm20) REVERT: R 11 GLN cc_start: 0.8602 (tt0) cc_final: 0.7838 (tp-100) REVERT: R 74 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7708 (tp-100) REVERT: R 92 ASP cc_start: 0.8395 (m-30) cc_final: 0.7973 (p0) REVERT: R 154 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8289 (t) REVERT: R 159 MET cc_start: 0.8342 (mtp) cc_final: 0.7863 (ttm) REVERT: S 24 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6821 (tm-30) REVERT: S 68 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8748 (mt-10) REVERT: S 75 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8494 (t0) REVERT: S 87 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6747 (pttp) REVERT: S 169 TYR cc_start: 0.7158 (t80) cc_final: 0.6745 (t80) REVERT: T 14 HIS cc_start: 0.8077 (t-90) cc_final: 0.7824 (t-90) REVERT: T 45 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7391 (p0) REVERT: T 102 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8818 (tm-30) REVERT: U 11 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8014 (tm-30) REVERT: U 18 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: U 86 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7867 (tp) REVERT: V 18 GLU cc_start: 0.8698 (tt0) cc_final: 0.8448 (tp30) REVERT: V 35 TYR cc_start: 0.8627 (m-80) cc_final: 0.8371 (m-10) REVERT: V 85 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: W 11 GLN cc_start: 0.8416 (tp40) cc_final: 0.7879 (pm20) REVERT: W 68 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8883 (tt0) REVERT: W 80 ARG cc_start: 0.9142 (mmm-85) cc_final: 0.8878 (mpt180) REVERT: W 92 ASP cc_start: 0.6741 (m-30) cc_final: 0.6250 (p0) REVERT: W 141 GLU cc_start: 0.8592 (mp0) cc_final: 0.8269 (tp30) REVERT: X 13 TYR cc_start: 0.6259 (t80) cc_final: 0.5802 (t80) REVERT: X 70 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8474 (mm) outliers start: 255 outliers final: 98 residues processed: 847 average time/residue: 1.2983 time to fit residues: 1336.2335 Evaluate side-chains 689 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 569 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 147 LYS Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 132 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 24 GLN C 126 ASN D 24 GLN F 22 ASN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 126 ASN I 76 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 140 ASN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS Q 75 ASN R 12 ASN R 14 HIS R 26 ASN ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 106 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 HIS ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 GLN X 106 HIS ** X 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34512 Z= 0.231 Angle : 0.630 11.154 46488 Z= 0.329 Chirality : 0.040 0.188 4896 Planarity : 0.004 0.065 6120 Dihedral : 4.276 23.578 4488 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.80 % Allowed : 27.99 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.52 (0.13), residues: 4080 helix: 2.38 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.80 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.013 0.001 HIS P 106 PHE 0.025 0.001 PHE R 133 TYR 0.020 0.002 TYR E 169 ARG 0.012 0.001 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 628 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9428 (t0) cc_final: 0.8814 (t0) REVERT: A 24 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: A 64 ARG cc_start: 0.8573 (ttt90) cc_final: 0.8197 (ttp-170) REVERT: A 76 GLN cc_start: 0.8359 (mt0) cc_final: 0.8141 (mt0) REVERT: B 24 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 58 HIS cc_start: 0.7258 (t70) cc_final: 0.6977 (t70) REVERT: B 76 GLN cc_start: 0.8503 (mt0) cc_final: 0.7998 (mt0) REVERT: B 109 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8624 (tppp) REVERT: C 13 TYR cc_start: 0.8016 (t80) cc_final: 0.7751 (t80) REVERT: C 45 ASP cc_start: 0.8482 (p0) cc_final: 0.7560 (t0) REVERT: C 86 ILE cc_start: 0.8865 (mt) cc_final: 0.8398 (tt) REVERT: C 90 ASP cc_start: 0.8396 (m-30) cc_final: 0.7869 (p0) REVERT: C 124 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5725 (p0) REVERT: C 127 ASP cc_start: 0.8168 (t0) cc_final: 0.7757 (t0) REVERT: C 138 TYR cc_start: 0.8756 (m-10) cc_final: 0.8527 (m-10) REVERT: C 159 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: D 16 ASP cc_start: 0.7591 (m-30) cc_final: 0.7090 (t0) REVERT: D 62 GLU cc_start: 0.7722 (mp0) cc_final: 0.7462 (mm-30) REVERT: D 75 ASN cc_start: 0.8285 (m-40) cc_final: 0.7996 (t0) REVERT: D 127 ASP cc_start: 0.7199 (t0) cc_final: 0.6300 (p0) REVERT: E 11 GLN cc_start: 0.8850 (tt0) cc_final: 0.8410 (tm130) REVERT: E 45 ASP cc_start: 0.7146 (p0) cc_final: 0.6189 (t70) REVERT: E 85 ASP cc_start: 0.7878 (m-30) cc_final: 0.7298 (p0) REVERT: E 92 ASP cc_start: 0.8658 (m-30) cc_final: 0.7947 (OUTLIER) REVERT: E 157 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7611 (ttp-110) REVERT: E 175 THR cc_start: 0.7810 (m) cc_final: 0.7535 (p) REVERT: F 38 MET cc_start: 0.8053 (mtp) cc_final: 0.7849 (ttm) REVERT: F 45 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7294 (p0) REVERT: F 47 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8923 (m) REVERT: F 80 ARG cc_start: 0.7787 (mmm160) cc_final: 0.7542 (mmp-170) REVERT: F 85 ASP cc_start: 0.8094 (m-30) cc_final: 0.7802 (m-30) REVERT: F 86 ILE cc_start: 0.8805 (mt) cc_final: 0.8508 (pp) REVERT: F 90 ASP cc_start: 0.8563 (m-30) cc_final: 0.8243 (p0) REVERT: F 92 ASP cc_start: 0.8426 (m-30) cc_final: 0.7389 (t0) REVERT: F 106 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7138 (t70) REVERT: F 117 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8289 (tp30) REVERT: G 45 ASP cc_start: 0.6205 (t0) cc_final: 0.5973 (t0) REVERT: G 76 GLN cc_start: 0.8093 (mt0) cc_final: 0.7837 (tp40) REVERT: G 106 HIS cc_start: 0.7356 (t70) cc_final: 0.6790 (m90) REVERT: H 46 ASP cc_start: 0.8434 (p0) cc_final: 0.7720 (t0) REVERT: H 65 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.9052 (mm-30) REVERT: H 86 ILE cc_start: 0.8171 (mt) cc_final: 0.7794 (tp) REVERT: H 127 ASP cc_start: 0.8390 (t0) cc_final: 0.8018 (t0) REVERT: I 18 GLU cc_start: 0.8810 (tt0) cc_final: 0.8550 (tt0) REVERT: I 90 ASP cc_start: 0.8237 (m-30) cc_final: 0.7417 (t0) REVERT: I 95 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8454 (tm-30) REVERT: J 24 GLN cc_start: 0.9010 (tp40) cc_final: 0.8446 (tm-30) REVERT: J 76 GLN cc_start: 0.8659 (mt0) cc_final: 0.8283 (mp10) REVERT: J 102 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7779 (tm-30) REVERT: K 51 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (t0) REVERT: K 86 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7847 (tp) REVERT: L 24 GLN cc_start: 0.8398 (tp40) cc_final: 0.8089 (tm-30) REVERT: L 84 GLN cc_start: 0.7848 (mm110) cc_final: 0.7519 (mm-40) REVERT: L 90 ASP cc_start: 0.7787 (m-30) cc_final: 0.6820 (p0) REVERT: L 102 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7768 (pp20) REVERT: L 113 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8644 (pt0) REVERT: M 63 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6781 (mm-30) REVERT: M 81 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7699 (pp) REVERT: M 84 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7641 (mm110) REVERT: N 86 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7806 (mm) REVERT: N 132 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: N 159 MET cc_start: 0.8166 (ttm) cc_final: 0.7882 (ttm) REVERT: O 80 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.6998 (ptm160) REVERT: O 169 TYR cc_start: 0.8507 (t80) cc_final: 0.8232 (t80) REVERT: P 43 ASP cc_start: 0.8508 (t70) cc_final: 0.8102 (t0) REVERT: P 51 ASN cc_start: 0.8530 (m110) cc_final: 0.8302 (m110) REVERT: P 64 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7652 (ttt-90) REVERT: P 68 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8592 (mp0) REVERT: Q 18 GLU cc_start: 0.9088 (tt0) cc_final: 0.8794 (tp30) REVERT: Q 24 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8401 (tp-100) REVERT: Q 95 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8114 (tp30) REVERT: Q 127 ASP cc_start: 0.8478 (t0) cc_final: 0.8268 (t0) REVERT: Q 169 TYR cc_start: 0.8872 (t80) cc_final: 0.8628 (t80) REVERT: R 8 GLN cc_start: 0.8594 (pt0) cc_final: 0.8312 (pm20) REVERT: R 11 GLN cc_start: 0.8594 (tt0) cc_final: 0.7813 (tm-30) REVERT: R 74 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7728 (tp-100) REVERT: R 77 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7454 (tpp80) REVERT: R 92 ASP cc_start: 0.8317 (m-30) cc_final: 0.7847 (p0) REVERT: R 154 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8118 (t) REVERT: R 159 MET cc_start: 0.8288 (mtp) cc_final: 0.7884 (ttm) REVERT: S 24 GLN cc_start: 0.7307 (tp-100) cc_final: 0.6815 (tm-30) REVERT: S 68 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8759 (mt-10) REVERT: S 87 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6612 (pttp) REVERT: T 14 HIS cc_start: 0.8118 (t-90) cc_final: 0.7865 (t-90) REVERT: T 102 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8826 (tm-30) REVERT: U 11 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: U 18 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: U 86 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8013 (tp) REVERT: V 11 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8177 (tp-100) REVERT: V 18 GLU cc_start: 0.8630 (tt0) cc_final: 0.8365 (tp30) REVERT: V 35 TYR cc_start: 0.8603 (m-80) cc_final: 0.8385 (m-10) REVERT: V 85 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: W 11 GLN cc_start: 0.8440 (tp40) cc_final: 0.7870 (pm20) REVERT: W 68 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8875 (tt0) REVERT: W 80 ARG cc_start: 0.9120 (mmm-85) cc_final: 0.8828 (mpt-90) REVERT: W 92 ASP cc_start: 0.6950 (m-30) cc_final: 0.6367 (p0) REVERT: W 141 GLU cc_start: 0.8560 (mp0) cc_final: 0.8287 (tp30) REVERT: W 147 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8334 (tttp) REVERT: W 149 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (mp) outliers start: 248 outliers final: 115 residues processed: 812 average time/residue: 1.2890 time to fit residues: 1269.2519 Evaluate side-chains 703 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 566 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 147 LYS Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 11 GLN Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 147 LYS Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 134 ILE Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 106 HIS B 26 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 74 GLN D 74 GLN D 99 ASN E 74 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 126 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 26 ASN ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS R 12 ASN R 14 HIS S 75 ASN S 110 ASN U 59 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 HIS ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34512 Z= 0.209 Angle : 0.620 11.683 46488 Z= 0.321 Chirality : 0.039 0.171 4896 Planarity : 0.004 0.067 6120 Dihedral : 4.238 23.707 4488 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.39 % Allowed : 29.17 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.74 (0.13), residues: 4080 helix: 2.55 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.75 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 94 HIS 0.013 0.001 HIS A 106 PHE 0.029 0.001 PHE F 133 TYR 0.022 0.002 TYR Q 169 ARG 0.012 0.001 ARG N 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 631 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9412 (t0) cc_final: 0.8753 (t0) REVERT: A 24 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 64 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8178 (ttp-170) REVERT: B 24 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 58 HIS cc_start: 0.7196 (t70) cc_final: 0.6943 (t70) REVERT: B 76 GLN cc_start: 0.8481 (mt0) cc_final: 0.7982 (mt0) REVERT: C 13 TYR cc_start: 0.8005 (t80) cc_final: 0.7742 (t80) REVERT: C 45 ASP cc_start: 0.8514 (p0) cc_final: 0.7694 (t0) REVERT: C 86 ILE cc_start: 0.8854 (mt) cc_final: 0.8405 (tt) REVERT: C 90 ASP cc_start: 0.8445 (m-30) cc_final: 0.7932 (p0) REVERT: C 124 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5567 (p0) REVERT: C 138 TYR cc_start: 0.8723 (m-10) cc_final: 0.8484 (m-10) REVERT: D 16 ASP cc_start: 0.7739 (m-30) cc_final: 0.7254 (t0) REVERT: D 62 GLU cc_start: 0.7709 (mp0) cc_final: 0.7453 (mm-30) REVERT: D 75 ASN cc_start: 0.8110 (m-40) cc_final: 0.7810 (t0) REVERT: D 127 ASP cc_start: 0.7168 (t0) cc_final: 0.6276 (p0) REVERT: E 11 GLN cc_start: 0.8867 (tt0) cc_final: 0.8463 (tm130) REVERT: E 45 ASP cc_start: 0.7031 (p0) cc_final: 0.6174 (t70) REVERT: E 85 ASP cc_start: 0.7872 (m-30) cc_final: 0.7309 (p0) REVERT: E 92 ASP cc_start: 0.8700 (m-30) cc_final: 0.8040 (t0) REVERT: E 157 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7581 (ttp-110) REVERT: E 175 THR cc_start: 0.7823 (m) cc_final: 0.7566 (p) REVERT: F 45 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7395 (p0) REVERT: F 47 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8920 (m) REVERT: F 62 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: F 80 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7575 (mmp-170) REVERT: F 86 ILE cc_start: 0.8944 (mt) cc_final: 0.8474 (pp) REVERT: F 90 ASP cc_start: 0.8461 (m-30) cc_final: 0.8175 (p0) REVERT: F 92 ASP cc_start: 0.8570 (m-30) cc_final: 0.7605 (t0) REVERT: F 106 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7090 (t70) REVERT: F 113 GLN cc_start: 0.9252 (tp40) cc_final: 0.8745 (tm-30) REVERT: G 59 GLN cc_start: 0.8898 (tp40) cc_final: 0.8623 (tp40) REVERT: G 76 GLN cc_start: 0.8040 (mt0) cc_final: 0.7560 (tp40) REVERT: G 106 HIS cc_start: 0.7383 (t70) cc_final: 0.6837 (m90) REVERT: H 46 ASP cc_start: 0.8405 (p0) cc_final: 0.7628 (t0) REVERT: H 65 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.9050 (mm-30) REVERT: H 86 ILE cc_start: 0.8136 (mt) cc_final: 0.7772 (tp) REVERT: H 127 ASP cc_start: 0.8361 (t0) cc_final: 0.8053 (t70) REVERT: I 90 ASP cc_start: 0.8320 (m-30) cc_final: 0.7527 (t0) REVERT: I 108 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: I 159 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: J 24 GLN cc_start: 0.9009 (tp40) cc_final: 0.8430 (tm-30) REVERT: J 102 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7779 (tm-30) REVERT: K 51 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (t0) REVERT: K 64 ARG cc_start: 0.8696 (tpp-160) cc_final: 0.8158 (tmm-80) REVERT: K 86 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8071 (tp) REVERT: L 84 GLN cc_start: 0.7811 (mm110) cc_final: 0.7521 (mm-40) REVERT: L 90 ASP cc_start: 0.7952 (m-30) cc_final: 0.6813 (p0) REVERT: L 102 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7764 (pp20) REVERT: L 113 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: L 134 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (tp) REVERT: M 81 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7678 (pp) REVERT: M 84 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7676 (mm110) REVERT: N 86 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7833 (mm) REVERT: N 132 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.6036 (m-30) REVERT: N 159 MET cc_start: 0.8200 (ttm) cc_final: 0.7814 (ttm) REVERT: N 163 GLU cc_start: 0.5965 (mp0) cc_final: 0.5573 (tm-30) REVERT: O 144 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8791 (ptpp) REVERT: O 159 MET cc_start: 0.7406 (ttp) cc_final: 0.6914 (ttm) REVERT: O 169 TYR cc_start: 0.8501 (t80) cc_final: 0.8205 (t80) REVERT: O 170 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8994 (tp) REVERT: P 43 ASP cc_start: 0.8585 (t70) cc_final: 0.8142 (t0) REVERT: P 51 ASN cc_start: 0.8569 (m110) cc_final: 0.8344 (m110) REVERT: P 68 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8557 (mp0) REVERT: Q 18 GLU cc_start: 0.9030 (tt0) cc_final: 0.8774 (tp30) REVERT: Q 24 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8336 (tm130) REVERT: Q 95 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8163 (tp30) REVERT: Q 127 ASP cc_start: 0.8539 (t0) cc_final: 0.8325 (t0) REVERT: Q 169 TYR cc_start: 0.8925 (t80) cc_final: 0.8668 (t80) REVERT: R 8 GLN cc_start: 0.8617 (pt0) cc_final: 0.8296 (pm20) REVERT: R 11 GLN cc_start: 0.8636 (tt0) cc_final: 0.7869 (tm-30) REVERT: R 77 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7548 (tpp80) REVERT: R 92 ASP cc_start: 0.8346 (m-30) cc_final: 0.7898 (p0) REVERT: R 154 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8120 (t) REVERT: R 159 MET cc_start: 0.8215 (mtp) cc_final: 0.7846 (ttm) REVERT: S 11 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7880 (tm-30) REVERT: S 24 GLN cc_start: 0.7399 (tp-100) cc_final: 0.7006 (tm-30) REVERT: S 68 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8765 (mt-10) REVERT: S 75 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8512 (t0) REVERT: S 87 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6835 (pttp) REVERT: T 14 HIS cc_start: 0.8148 (t-90) cc_final: 0.7859 (t-90) REVERT: T 102 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8914 (tm-30) REVERT: T 159 MET cc_start: 0.7122 (mtp) cc_final: 0.6594 (mtp) REVERT: U 11 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8114 (tm-30) REVERT: U 18 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: U 80 ARG cc_start: 0.7905 (mpt-90) cc_final: 0.7325 (mpt90) REVERT: U 86 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8014 (tp) REVERT: V 18 GLU cc_start: 0.8620 (tt0) cc_final: 0.8378 (tp30) REVERT: V 74 GLN cc_start: 0.8551 (tp40) cc_final: 0.8297 (tp40) REVERT: V 85 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: W 11 GLN cc_start: 0.8333 (tp40) cc_final: 0.7771 (pm20) REVERT: W 92 ASP cc_start: 0.6917 (m-30) cc_final: 0.6351 (p0) REVERT: W 141 GLU cc_start: 0.8568 (mp0) cc_final: 0.8288 (tp30) REVERT: W 149 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8226 (mp) outliers start: 233 outliers final: 104 residues processed: 804 average time/residue: 1.2253 time to fit residues: 1203.3458 Evaluate side-chains 688 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 558 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain O residue 144 LYS Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 99 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 126 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 26 ASN ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS Q 155 ASN R 12 ASN R 14 HIS ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN U 74 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34512 Z= 0.219 Angle : 0.654 11.568 46488 Z= 0.336 Chirality : 0.039 0.180 4896 Planarity : 0.004 0.069 6120 Dihedral : 4.254 23.393 4488 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.03 % Allowed : 30.18 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.78 (0.13), residues: 4080 helix: 2.58 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.74 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.013 0.001 HIS P 106 PHE 0.032 0.001 PHE F 133 TYR 0.028 0.002 TYR I 169 ARG 0.016 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 628 time to evaluate : 4.084 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: A 12 ASN cc_start: 0.9413 (t0) cc_final: 0.8730 (t0) REVERT: A 24 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: A 64 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8167 (ttp-170) REVERT: B 24 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 58 HIS cc_start: 0.7188 (t70) cc_final: 0.6921 (t70) REVERT: B 76 GLN cc_start: 0.8472 (mt0) cc_final: 0.7989 (mt0) REVERT: C 13 TYR cc_start: 0.8033 (t80) cc_final: 0.7767 (t80) REVERT: C 45 ASP cc_start: 0.8627 (p0) cc_final: 0.7867 (t0) REVERT: C 86 ILE cc_start: 0.8860 (mt) cc_final: 0.8419 (tt) REVERT: C 90 ASP cc_start: 0.8456 (m-30) cc_final: 0.7995 (p0) REVERT: C 124 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5553 (p0) REVERT: C 138 TYR cc_start: 0.8718 (m-10) cc_final: 0.8487 (m-10) REVERT: D 16 ASP cc_start: 0.7740 (m-30) cc_final: 0.7248 (t0) REVERT: D 43 ASP cc_start: 0.9539 (t70) cc_final: 0.9101 (t0) REVERT: D 62 GLU cc_start: 0.7704 (mp0) cc_final: 0.7453 (mm-30) REVERT: D 75 ASN cc_start: 0.8072 (m-40) cc_final: 0.7827 (t0) REVERT: D 127 ASP cc_start: 0.7152 (t0) cc_final: 0.6258 (p0) REVERT: E 11 GLN cc_start: 0.8868 (tt0) cc_final: 0.8470 (tm130) REVERT: E 45 ASP cc_start: 0.7032 (p0) cc_final: 0.5933 (t0) REVERT: E 85 ASP cc_start: 0.7861 (m-30) cc_final: 0.7271 (p0) REVERT: E 92 ASP cc_start: 0.8746 (m-30) cc_final: 0.8095 (t0) REVERT: E 157 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7570 (ttp-110) REVERT: E 175 THR cc_start: 0.7868 (m) cc_final: 0.7618 (p) REVERT: F 45 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7420 (p0) REVERT: F 62 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: F 86 ILE cc_start: 0.8916 (mt) cc_final: 0.8669 (pt) REVERT: F 90 ASP cc_start: 0.8472 (m-30) cc_final: 0.8206 (p0) REVERT: F 92 ASP cc_start: 0.8618 (m-30) cc_final: 0.7661 (t0) REVERT: F 106 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7056 (t70) REVERT: F 113 GLN cc_start: 0.9257 (tp40) cc_final: 0.8767 (tm-30) REVERT: F 169 TYR cc_start: 0.8639 (t80) cc_final: 0.8260 (t80) REVERT: G 11 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8264 (tp-100) REVERT: G 59 GLN cc_start: 0.8903 (tp40) cc_final: 0.8648 (tp40) REVERT: G 72 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7745 (tmmm) REVERT: G 106 HIS cc_start: 0.7383 (t70) cc_final: 0.6827 (m90) REVERT: H 46 ASP cc_start: 0.8410 (p0) cc_final: 0.7713 (t0) REVERT: H 65 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.9049 (mm-30) REVERT: H 86 ILE cc_start: 0.8179 (mt) cc_final: 0.7789 (tp) REVERT: H 90 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: H 127 ASP cc_start: 0.8359 (t0) cc_final: 0.8021 (t70) REVERT: I 18 GLU cc_start: 0.8765 (tt0) cc_final: 0.8439 (tt0) REVERT: I 90 ASP cc_start: 0.8318 (m-30) cc_final: 0.7523 (t0) REVERT: I 108 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: I 154 THR cc_start: 0.8925 (t) cc_final: 0.8711 (t) REVERT: I 159 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7265 (mmm) REVERT: J 24 GLN cc_start: 0.9004 (tp40) cc_final: 0.8428 (tm-30) REVERT: J 102 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7784 (tm-30) REVERT: K 51 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7973 (t0) REVERT: K 64 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8194 (tmm-80) REVERT: L 84 GLN cc_start: 0.7936 (mm110) cc_final: 0.7653 (mm-40) REVERT: L 90 ASP cc_start: 0.7959 (m-30) cc_final: 0.6663 (p0) REVERT: L 102 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7765 (pp20) REVERT: L 113 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: M 75 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8163 (t0) REVERT: M 84 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7692 (mm110) REVERT: N 86 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (mm) REVERT: N 132 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6050 (m-30) REVERT: N 159 MET cc_start: 0.8209 (ttm) cc_final: 0.7837 (ttm) REVERT: N 163 GLU cc_start: 0.5994 (mp0) cc_final: 0.5631 (tm-30) REVERT: O 40 TYR cc_start: 0.8225 (m-80) cc_final: 0.8005 (m-10) REVERT: O 80 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.6985 (ptm160) REVERT: O 96 SER cc_start: 0.7480 (m) cc_final: 0.7260 (m) REVERT: O 159 MET cc_start: 0.7483 (ttp) cc_final: 0.6966 (ttm) REVERT: O 169 TYR cc_start: 0.8494 (t80) cc_final: 0.8181 (t80) REVERT: O 170 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8980 (tp) REVERT: P 43 ASP cc_start: 0.8695 (t70) cc_final: 0.8261 (t0) REVERT: P 51 ASN cc_start: 0.8581 (m110) cc_final: 0.8371 (m110) REVERT: P 68 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8504 (mp0) REVERT: P 159 MET cc_start: 0.7925 (ttp) cc_final: 0.7710 (ttp) REVERT: Q 18 GLU cc_start: 0.8979 (tt0) cc_final: 0.8704 (tp30) REVERT: Q 95 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8154 (tp30) REVERT: Q 169 TYR cc_start: 0.8989 (t80) cc_final: 0.8636 (t80) REVERT: R 8 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: R 11 GLN cc_start: 0.8649 (tt0) cc_final: 0.7880 (tm-30) REVERT: R 77 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7493 (tpp80) REVERT: R 85 ASP cc_start: 0.8118 (m-30) cc_final: 0.7517 (t0) REVERT: R 92 ASP cc_start: 0.8410 (m-30) cc_final: 0.8001 (p0) REVERT: R 154 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7937 (t) REVERT: S 11 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7967 (tm-30) REVERT: S 13 TYR cc_start: 0.7844 (t80) cc_final: 0.7577 (t80) REVERT: S 24 GLN cc_start: 0.7404 (tp-100) cc_final: 0.7009 (tm-30) REVERT: S 86 ILE cc_start: 0.8473 (mm) cc_final: 0.8110 (tp) REVERT: S 87 LYS cc_start: 0.7346 (mmtt) cc_final: 0.6798 (pttp) REVERT: T 14 HIS cc_start: 0.8144 (t-90) cc_final: 0.7882 (t-90) REVERT: T 102 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8917 (tm-30) REVERT: U 18 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: U 80 ARG cc_start: 0.7956 (mpt-90) cc_final: 0.7321 (mpt90) REVERT: U 86 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7894 (tp) REVERT: V 18 GLU cc_start: 0.8600 (tt0) cc_final: 0.8359 (tp30) REVERT: V 74 GLN cc_start: 0.8536 (tp40) cc_final: 0.8282 (tp40) REVERT: V 85 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: V 107 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8530 (tm) REVERT: W 11 GLN cc_start: 0.8336 (tp40) cc_final: 0.7762 (pm20) REVERT: W 14 HIS cc_start: 0.7487 (t-90) cc_final: 0.7240 (t-90) REVERT: W 92 ASP cc_start: 0.6956 (m-30) cc_final: 0.6382 (p0) REVERT: W 141 GLU cc_start: 0.8515 (mp0) cc_final: 0.8274 (tp30) REVERT: W 147 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8339 (tttp) REVERT: W 149 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8234 (mp) outliers start: 220 outliers final: 111 residues processed: 784 average time/residue: 1.2802 time to fit residues: 1234.2507 Evaluate side-chains 708 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 570 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain Q residue 74 GLN Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 144 LYS Chi-restraints excluded: chain R residue 8 GLN Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 147 LYS Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 106 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 99 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN I 76 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS M 99 ASN ** M 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 26 ASN ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 ASN Q 113 GLN R 12 ASN R 14 HIS ** S 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 84 GLN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34512 Z= 0.206 Angle : 0.660 12.347 46488 Z= 0.337 Chirality : 0.039 0.172 4896 Planarity : 0.004 0.091 6120 Dihedral : 4.237 26.706 4488 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.18 % Allowed : 31.74 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.89 (0.13), residues: 4080 helix: 2.66 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.74 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 94 HIS 0.024 0.001 HIS A 106 PHE 0.028 0.001 PHE F 133 TYR 0.021 0.002 TYR K 169 ARG 0.020 0.001 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 630 time to evaluate : 4.137 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: A 12 ASN cc_start: 0.9425 (t0) cc_final: 0.8742 (t0) REVERT: A 24 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 64 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8164 (ttp-170) REVERT: B 24 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 58 HIS cc_start: 0.7189 (t70) cc_final: 0.6921 (t70) REVERT: B 76 GLN cc_start: 0.8336 (mt0) cc_final: 0.7869 (mt0) REVERT: C 45 ASP cc_start: 0.8615 (p0) cc_final: 0.7847 (t0) REVERT: C 86 ILE cc_start: 0.8858 (mt) cc_final: 0.8430 (tt) REVERT: C 90 ASP cc_start: 0.8352 (m-30) cc_final: 0.7876 (p0) REVERT: C 124 ASP cc_start: 0.5962 (OUTLIER) cc_final: 0.5539 (p0) REVERT: C 138 TYR cc_start: 0.8702 (m-10) cc_final: 0.8466 (m-10) REVERT: D 16 ASP cc_start: 0.7724 (m-30) cc_final: 0.7233 (t0) REVERT: D 62 GLU cc_start: 0.7692 (mp0) cc_final: 0.7449 (mm-30) REVERT: D 75 ASN cc_start: 0.8111 (m-40) cc_final: 0.7876 (t0) REVERT: D 127 ASP cc_start: 0.7067 (t0) cc_final: 0.6189 (p0) REVERT: E 11 GLN cc_start: 0.8874 (tt0) cc_final: 0.8476 (tm130) REVERT: E 45 ASP cc_start: 0.7063 (p0) cc_final: 0.5834 (t0) REVERT: E 85 ASP cc_start: 0.7879 (m-30) cc_final: 0.7313 (p0) REVERT: E 92 ASP cc_start: 0.8761 (m-30) cc_final: 0.8139 (t0) REVERT: E 157 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7538 (ttp-110) REVERT: E 175 THR cc_start: 0.7906 (m) cc_final: 0.7653 (p) REVERT: F 24 GLN cc_start: 0.7796 (tm130) cc_final: 0.7488 (tm-30) REVERT: F 45 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7467 (p0) REVERT: F 86 ILE cc_start: 0.9002 (mt) cc_final: 0.8661 (pt) REVERT: F 90 ASP cc_start: 0.8482 (m-30) cc_final: 0.8229 (p0) REVERT: F 92 ASP cc_start: 0.8534 (m-30) cc_final: 0.7660 (t0) REVERT: F 113 GLN cc_start: 0.9256 (tp40) cc_final: 0.8761 (tm-30) REVERT: F 169 TYR cc_start: 0.8707 (t80) cc_final: 0.8352 (t80) REVERT: G 11 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8284 (tp-100) REVERT: G 59 GLN cc_start: 0.8890 (tp40) cc_final: 0.8628 (tp40) REVERT: G 94 TRP cc_start: 0.8580 (m100) cc_final: 0.8181 (m100) REVERT: G 106 HIS cc_start: 0.7369 (t70) cc_final: 0.6805 (m90) REVERT: H 46 ASP cc_start: 0.8399 (p0) cc_final: 0.7691 (t0) REVERT: H 65 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.9044 (mm-30) REVERT: H 86 ILE cc_start: 0.8167 (mt) cc_final: 0.7773 (tp) REVERT: H 127 ASP cc_start: 0.8437 (t0) cc_final: 0.8128 (t70) REVERT: I 18 GLU cc_start: 0.8846 (tt0) cc_final: 0.8568 (tt0) REVERT: I 47 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8574 (t) REVERT: I 90 ASP cc_start: 0.8326 (m-30) cc_final: 0.7522 (t0) REVERT: I 108 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: I 154 THR cc_start: 0.8992 (t) cc_final: 0.8774 (t) REVERT: J 24 GLN cc_start: 0.8997 (tp40) cc_final: 0.8414 (tm-30) REVERT: J 102 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7775 (tm-30) REVERT: K 51 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7970 (t0) REVERT: K 64 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8196 (tmm-80) REVERT: L 84 GLN cc_start: 0.7960 (mm110) cc_final: 0.7698 (mm-40) REVERT: L 90 ASP cc_start: 0.8021 (m-30) cc_final: 0.6680 (p0) REVERT: L 102 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7762 (pp20) REVERT: L 113 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: M 81 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7526 (pp) REVERT: N 132 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.6083 (m-30) REVERT: N 159 MET cc_start: 0.8131 (ttm) cc_final: 0.7773 (ttm) REVERT: O 80 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.6989 (ptm160) REVERT: O 96 SER cc_start: 0.7394 (m) cc_final: 0.7161 (m) REVERT: O 108 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: O 169 TYR cc_start: 0.8452 (t80) cc_final: 0.8187 (t80) REVERT: O 170 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8997 (tp) REVERT: P 43 ASP cc_start: 0.8633 (t70) cc_final: 0.8152 (t0) REVERT: P 51 ASN cc_start: 0.8578 (m110) cc_final: 0.8352 (m110) REVERT: P 68 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8493 (mp0) REVERT: Q 18 GLU cc_start: 0.8877 (tt0) cc_final: 0.8666 (tp30) REVERT: Q 95 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8164 (tp30) REVERT: Q 169 TYR cc_start: 0.8968 (t80) cc_final: 0.8659 (t80) REVERT: R 8 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: R 11 GLN cc_start: 0.8649 (tt0) cc_final: 0.7880 (tm-30) REVERT: R 77 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7500 (tpp80) REVERT: R 85 ASP cc_start: 0.8178 (m-30) cc_final: 0.7587 (t0) REVERT: R 92 ASP cc_start: 0.8466 (m-30) cc_final: 0.8083 (p0) REVERT: R 154 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8065 (t) REVERT: S 13 TYR cc_start: 0.7871 (t80) cc_final: 0.7560 (t80) REVERT: S 86 ILE cc_start: 0.8447 (mm) cc_final: 0.8104 (tp) REVERT: S 87 LYS cc_start: 0.7352 (mmtt) cc_final: 0.6798 (pttp) REVERT: T 14 HIS cc_start: 0.8116 (t-90) cc_final: 0.7864 (t-90) REVERT: T 38 MET cc_start: 0.8622 (tpp) cc_final: 0.8316 (mmm) REVERT: T 102 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8920 (tm-30) REVERT: U 18 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: U 80 ARG cc_start: 0.7953 (mpt-90) cc_final: 0.7336 (mpt90) REVERT: U 86 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7877 (tp) REVERT: U 116 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8360 (mm) REVERT: V 85 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8491 (m-30) REVERT: V 107 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8499 (tm) REVERT: W 11 GLN cc_start: 0.8336 (tp40) cc_final: 0.7761 (pm20) REVERT: W 92 ASP cc_start: 0.6948 (m-30) cc_final: 0.6352 (p0) REVERT: W 141 GLU cc_start: 0.8477 (mp0) cc_final: 0.8251 (tp30) REVERT: W 147 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8324 (tttp) REVERT: W 149 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (mp) outliers start: 189 outliers final: 98 residues processed: 772 average time/residue: 1.2558 time to fit residues: 1182.2293 Evaluate side-chains 684 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 562 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 140 ASN Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain R residue 8 GLN Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 172 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 147 LYS Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 24 GLN E 99 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 126 ASN H 24 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 51 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS M 99 ASN ** M 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN O 140 ASN P 24 GLN P 106 HIS Q 74 GLN R 12 ASN R 14 HIS T 66 HIS ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 GLN U 74 GLN U 119 HIS ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 ASN X 24 GLN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34512 Z= 0.255 Angle : 0.706 13.373 46488 Z= 0.361 Chirality : 0.041 0.173 4896 Planarity : 0.004 0.074 6120 Dihedral : 4.321 27.332 4488 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.69 % Allowed : 33.20 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.70 (0.13), residues: 4080 helix: 2.57 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -0.88 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 94 HIS 0.019 0.001 HIS R 152 PHE 0.037 0.002 PHE F 133 TYR 0.024 0.002 TYR K 169 ARG 0.017 0.001 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 608 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: A 64 ARG cc_start: 0.8517 (ttt90) cc_final: 0.8191 (ttp-170) REVERT: B 24 GLN cc_start: 0.8577 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 58 HIS cc_start: 0.7301 (t70) cc_final: 0.7023 (t70) REVERT: C 45 ASP cc_start: 0.8675 (p0) cc_final: 0.7943 (t0) REVERT: C 86 ILE cc_start: 0.8858 (mt) cc_final: 0.8421 (tt) REVERT: C 90 ASP cc_start: 0.8357 (m-30) cc_final: 0.7877 (p0) REVERT: C 124 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5864 (p0) REVERT: C 138 TYR cc_start: 0.8773 (m-10) cc_final: 0.8545 (m-10) REVERT: D 16 ASP cc_start: 0.7772 (m-30) cc_final: 0.7289 (t0) REVERT: D 43 ASP cc_start: 0.9568 (t70) cc_final: 0.9165 (t0) REVERT: D 62 GLU cc_start: 0.7565 (mp0) cc_final: 0.7317 (mm-30) REVERT: D 127 ASP cc_start: 0.6854 (t0) cc_final: 0.5909 (p0) REVERT: E 11 GLN cc_start: 0.8870 (tt0) cc_final: 0.8440 (tm130) REVERT: E 45 ASP cc_start: 0.7159 (p0) cc_final: 0.6273 (t0) REVERT: E 85 ASP cc_start: 0.7941 (m-30) cc_final: 0.7389 (p0) REVERT: E 92 ASP cc_start: 0.8748 (m-30) cc_final: 0.8134 (t0) REVERT: E 157 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7570 (ttp-110) REVERT: F 45 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7697 (p0) REVERT: F 90 ASP cc_start: 0.8440 (m-30) cc_final: 0.8204 (p0) REVERT: F 92 ASP cc_start: 0.8525 (m-30) cc_final: 0.7759 (t0) REVERT: F 106 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.7065 (t70) REVERT: F 113 GLN cc_start: 0.9240 (tp40) cc_final: 0.8759 (tm-30) REVERT: F 169 TYR cc_start: 0.8838 (t80) cc_final: 0.8436 (t80) REVERT: G 59 GLN cc_start: 0.8974 (tp40) cc_final: 0.8732 (tp40) REVERT: G 94 TRP cc_start: 0.8554 (m100) cc_final: 0.8215 (m100) REVERT: G 106 HIS cc_start: 0.7408 (t70) cc_final: 0.6828 (m90) REVERT: H 46 ASP cc_start: 0.8538 (p0) cc_final: 0.7726 (t0) REVERT: H 65 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9060 (mm-30) REVERT: H 86 ILE cc_start: 0.8255 (mt) cc_final: 0.7849 (tp) REVERT: H 127 ASP cc_start: 0.8655 (t0) cc_final: 0.8325 (t70) REVERT: I 47 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8608 (t) REVERT: I 80 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7667 (mmt90) REVERT: I 90 ASP cc_start: 0.8328 (m-30) cc_final: 0.7552 (t0) REVERT: I 108 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: I 154 THR cc_start: 0.8996 (t) cc_final: 0.8777 (t) REVERT: J 24 GLN cc_start: 0.9012 (tp40) cc_final: 0.8442 (tm-30) REVERT: J 102 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7793 (tm-30) REVERT: K 51 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8061 (t0) REVERT: K 64 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8247 (tmm-80) REVERT: K 70 LEU cc_start: 0.8366 (mt) cc_final: 0.8154 (mp) REVERT: L 84 GLN cc_start: 0.7878 (mm110) cc_final: 0.7643 (mm-40) REVERT: L 90 ASP cc_start: 0.8129 (m-30) cc_final: 0.6900 (p0) REVERT: L 102 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7836 (pp20) REVERT: L 113 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8572 (pt0) REVERT: M 11 GLN cc_start: 0.8871 (tp40) cc_final: 0.8660 (tp-100) REVERT: M 81 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7540 (pp) REVERT: M 84 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7603 (mm110) REVERT: M 85 ASP cc_start: 0.7743 (m-30) cc_final: 0.7391 (t0) REVERT: N 132 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.5268 (m-30) REVERT: N 159 MET cc_start: 0.8242 (ttm) cc_final: 0.7888 (ttm) REVERT: O 80 ARG cc_start: 0.7812 (mmt-90) cc_final: 0.7045 (ptm160) REVERT: O 96 SER cc_start: 0.7502 (m) cc_final: 0.7281 (m) REVERT: O 108 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: O 169 TYR cc_start: 0.8514 (t80) cc_final: 0.8196 (t80) REVERT: O 170 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9069 (tp) REVERT: P 43 ASP cc_start: 0.8785 (t70) cc_final: 0.8378 (t0) REVERT: P 51 ASN cc_start: 0.8651 (m110) cc_final: 0.8430 (m110) REVERT: P 68 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8735 (mt-10) REVERT: Q 18 GLU cc_start: 0.8872 (tt0) cc_final: 0.8659 (tp30) REVERT: Q 95 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8149 (tp30) REVERT: R 11 GLN cc_start: 0.8541 (tt0) cc_final: 0.7992 (tm-30) REVERT: R 77 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7538 (tpp80) REVERT: R 92 ASP cc_start: 0.8392 (m-30) cc_final: 0.8160 (p0) REVERT: R 154 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7989 (t) REVERT: S 86 ILE cc_start: 0.8454 (mm) cc_final: 0.8089 (tp) REVERT: S 87 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6549 (pttp) REVERT: T 38 MET cc_start: 0.8675 (tpp) cc_final: 0.8374 (mmm) REVERT: T 102 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8927 (tm-30) REVERT: U 11 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8201 (tm-30) REVERT: U 18 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: U 80 ARG cc_start: 0.7992 (mpt-90) cc_final: 0.7374 (mpt90) REVERT: U 86 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7926 (tp) REVERT: U 116 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (mm) REVERT: V 71 MET cc_start: 0.8214 (ttm) cc_final: 0.7904 (tmm) REVERT: V 85 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: V 107 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8549 (tm) REVERT: W 11 GLN cc_start: 0.8442 (tp40) cc_final: 0.7841 (pm20) REVERT: W 92 ASP cc_start: 0.6876 (m-30) cc_final: 0.6314 (p0) REVERT: W 141 GLU cc_start: 0.8510 (mp0) cc_final: 0.8273 (tp30) REVERT: W 147 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8335 (tttp) REVERT: W 149 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8241 (mp) outliers start: 171 outliers final: 95 residues processed: 734 average time/residue: 1.2719 time to fit residues: 1138.0728 Evaluate side-chains 676 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 558 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 106 HIS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 58 HIS Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain P residue 172 ASP Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 147 LYS Chi-restraints excluded: chain W residue 149 LEU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 0.0020 chunk 236 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 8.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 overall best weight: 1.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 22 ASN C 24 GLN D 24 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN H 75 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS M 99 ASN ** M 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN O 24 GLN O 26 ASN O 140 ASN P 24 GLN P 106 HIS ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 HIS X 22 ASN X 24 GLN X 76 GLN X 155 ASN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34512 Z= 0.182 Angle : 0.688 12.731 46488 Z= 0.346 Chirality : 0.038 0.193 4896 Planarity : 0.004 0.076 6120 Dihedral : 4.196 27.184 4488 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.18 % Allowed : 34.98 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.06 (0.13), residues: 4080 helix: 2.81 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -0.78 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.014 0.001 HIS P 106 PHE 0.028 0.001 PHE R 133 TYR 0.027 0.002 TYR G 41 ARG 0.016 0.001 ARG P 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 700 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8491 (ttt90) cc_final: 0.8239 (tmm-80) REVERT: A 164 SER cc_start: 0.7635 (t) cc_final: 0.7160 (p) REVERT: B 24 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 58 HIS cc_start: 0.7065 (t70) cc_final: 0.6799 (t70) REVERT: B 76 GLN cc_start: 0.8227 (mt0) cc_final: 0.7810 (mt0) REVERT: C 45 ASP cc_start: 0.8579 (p0) cc_final: 0.7843 (t0) REVERT: C 68 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8309 (tm-30) REVERT: C 86 ILE cc_start: 0.8832 (mt) cc_final: 0.8454 (tt) REVERT: C 124 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5279 (p0) REVERT: C 138 TYR cc_start: 0.8596 (m-10) cc_final: 0.8321 (m-10) REVERT: D 16 ASP cc_start: 0.7672 (m-30) cc_final: 0.7197 (t0) REVERT: D 62 GLU cc_start: 0.7654 (mp0) cc_final: 0.7410 (mm-30) REVERT: D 127 ASP cc_start: 0.6904 (t0) cc_final: 0.6140 (p0) REVERT: E 11 GLN cc_start: 0.8885 (tt0) cc_final: 0.8486 (tm130) REVERT: E 45 ASP cc_start: 0.6961 (p0) cc_final: 0.5788 (t0) REVERT: E 85 ASP cc_start: 0.7888 (m-30) cc_final: 0.7435 (p0) REVERT: E 92 ASP cc_start: 0.8774 (m-30) cc_final: 0.8134 (t0) REVERT: F 43 ASP cc_start: 0.8815 (t0) cc_final: 0.8546 (t0) REVERT: F 45 ASP cc_start: 0.8202 (p0) cc_final: 0.7589 (p0) REVERT: F 80 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7956 (mmp80) REVERT: F 90 ASP cc_start: 0.8453 (m-30) cc_final: 0.8221 (p0) REVERT: F 92 ASP cc_start: 0.8568 (m-30) cc_final: 0.7798 (t0) REVERT: F 107 LEU cc_start: 0.8204 (pp) cc_final: 0.7918 (pp) REVERT: F 113 GLN cc_start: 0.9244 (tp40) cc_final: 0.8720 (tm-30) REVERT: F 169 TYR cc_start: 0.8614 (t80) cc_final: 0.8301 (t80) REVERT: G 106 HIS cc_start: 0.7275 (t70) cc_final: 0.6796 (m170) REVERT: H 46 ASP cc_start: 0.8320 (p0) cc_final: 0.7630 (t0) REVERT: H 65 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.9031 (mm-30) REVERT: H 75 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (t0) REVERT: H 86 ILE cc_start: 0.8137 (mt) cc_final: 0.7779 (tp) REVERT: H 127 ASP cc_start: 0.8646 (t0) cc_final: 0.8381 (t70) REVERT: H 130 LEU cc_start: 0.8848 (tt) cc_final: 0.8454 (tp) REVERT: I 80 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7942 (mmt90) REVERT: I 90 ASP cc_start: 0.8448 (m-30) cc_final: 0.7782 (t0) REVERT: I 108 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: I 154 THR cc_start: 0.8929 (t) cc_final: 0.8582 (t) REVERT: J 24 GLN cc_start: 0.8969 (tp40) cc_final: 0.8495 (tm-30) REVERT: J 102 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7571 (tm-30) REVERT: K 51 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7886 (t0) REVERT: K 64 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8223 (tmm-80) REVERT: K 70 LEU cc_start: 0.8260 (mt) cc_final: 0.8031 (mp) REVERT: K 80 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7533 (mmm160) REVERT: L 84 GLN cc_start: 0.7832 (mm110) cc_final: 0.7620 (mm-40) REVERT: L 90 ASP cc_start: 0.8098 (m-30) cc_final: 0.6625 (p0) REVERT: L 102 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7705 (pp20) REVERT: L 113 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: M 11 GLN cc_start: 0.8873 (tp40) cc_final: 0.8669 (tp-100) REVERT: M 63 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6949 (mm-30) REVERT: M 84 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7777 (mm110) REVERT: N 159 MET cc_start: 0.8122 (ttm) cc_final: 0.7818 (ttm) REVERT: O 96 SER cc_start: 0.7062 (m) cc_final: 0.6361 (p) REVERT: P 68 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8751 (mt-10) REVERT: P 169 TYR cc_start: 0.8712 (t80) cc_final: 0.8494 (t80) REVERT: Q 95 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8158 (tp30) REVERT: Q 169 TYR cc_start: 0.8834 (t80) cc_final: 0.8610 (t80) REVERT: R 8 GLN cc_start: 0.8509 (pt0) cc_final: 0.8243 (pm20) REVERT: R 11 GLN cc_start: 0.8556 (tt0) cc_final: 0.7980 (tm-30) REVERT: R 55 TYR cc_start: 0.8098 (t80) cc_final: 0.7602 (OUTLIER) REVERT: R 77 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7420 (tpp80) REVERT: R 80 ARG cc_start: 0.7627 (mmm160) cc_final: 0.6708 (mpt-90) REVERT: R 85 ASP cc_start: 0.8033 (m-30) cc_final: 0.7628 (t0) REVERT: R 154 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8041 (t) REVERT: S 13 TYR cc_start: 0.7819 (t80) cc_final: 0.7569 (t80) REVERT: S 68 GLU cc_start: 0.8454 (mp0) cc_final: 0.8070 (mp0) REVERT: S 86 ILE cc_start: 0.8464 (mm) cc_final: 0.8210 (tp) REVERT: S 87 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6589 (pttp) REVERT: T 14 HIS cc_start: 0.8073 (t-90) cc_final: 0.7839 (t-90) REVERT: T 102 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8965 (tm-30) REVERT: U 11 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8193 (tm-30) REVERT: U 18 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: U 80 ARG cc_start: 0.8053 (mpt-90) cc_final: 0.7427 (mpt90) REVERT: U 86 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7813 (tp) REVERT: V 18 GLU cc_start: 0.8245 (pt0) cc_final: 0.7994 (pm20) REVERT: V 71 MET cc_start: 0.8174 (ttm) cc_final: 0.7839 (tmm) REVERT: V 85 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: W 11 GLN cc_start: 0.8401 (tp40) cc_final: 0.7799 (pm20) REVERT: W 44 ARG cc_start: 0.7325 (mtp180) cc_final: 0.7021 (mtp180) REVERT: W 92 ASP cc_start: 0.6853 (m-30) cc_final: 0.6333 (p0) REVERT: W 141 GLU cc_start: 0.8401 (mp0) cc_final: 0.8195 (tp30) REVERT: W 147 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8308 (tttp) REVERT: X 13 TYR cc_start: 0.7603 (t80) cc_final: 0.7006 (t80) REVERT: X 24 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: X 138 TYR cc_start: 0.7981 (m-80) cc_final: 0.7695 (m-80) outliers start: 116 outliers final: 53 residues processed: 780 average time/residue: 1.2509 time to fit residues: 1187.9568 Evaluate side-chains 670 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 605 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain K residue 51 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 12 ASN Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 18 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 118 LEU Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 75 ASN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 131 CYS Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 42 PHE Chi-restraints excluded: chain W residue 147 LYS Chi-restraints excluded: chain W residue 173 LYS Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 0.0040 chunk 332 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 112 ASN C 24 GLN D 24 GLN D 51 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 155 ASN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN H 24 GLN H 75 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN ** I 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN K 51 ASN K 84 GLN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS L 129 HIS M 99 ASN M 110 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 ASN ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 GLN P 106 HIS P 140 ASN R 12 ASN S 24 GLN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** V 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 74 GLN ** X 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.114667 restraints weight = 69638.459| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.97 r_work: 0.3674 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34512 Z= 0.194 Angle : 0.702 12.597 46488 Z= 0.353 Chirality : 0.038 0.223 4896 Planarity : 0.004 0.075 6120 Dihedral : 4.199 27.433 4488 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.82 % Allowed : 36.49 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.04 (0.13), residues: 4080 helix: 2.84 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -0.86 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 94 HIS 0.014 0.001 HIS P 106 PHE 0.029 0.001 PHE R 133 TYR 0.030 0.002 TYR I 169 ARG 0.017 0.001 ARG N 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18281.83 seconds wall clock time: 323 minutes 10.64 seconds (19390.64 seconds total)