Starting phenix.real_space_refine on Fri Mar 22 14:11:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fes_31562/03_2024/7fes_31562.pdb" } resolution = 3.4 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= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 10641 2.51 5 N 2819 2.21 5 O 3220 1.98 5 H 17095 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 37": "OD1" <-> "OD2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "C ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "E ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 147": "OD1" <-> "OD2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 177": "OE1" <-> "OE2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L ASP 37": "OD1" <-> "OD2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 171": "OD1" <-> "OD2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M ASP 54": "OD1" <-> "OD2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ASP 169": "OD1" <-> "OD2" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33873 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2402 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2411 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2426 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2419 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2418 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2380 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "M" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2463 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Chain: "N" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2422 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 13.90, per 1000 atoms: 0.41 Number of scatterers: 33873 At special positions: 0 Unit cell: (120.4, 123.84, 102.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 3220 8.00 N 2819 7.00 C 10641 6.00 H 17095 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.33 Conformation dependent library (CDL) restraints added in 3.3 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 18 sheets defined 49.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.679A pdb=" N LYS A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.614A pdb=" N ALA A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 4.210A pdb=" N MET A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.888A pdb=" N LEU A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.588A pdb=" N ILE A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.518A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 36 through 53 removed outlier: 3.704A pdb=" N ALA B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 4.105A pdb=" N MET B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.986A pdb=" N LEU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.680A pdb=" N ASP B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.586A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.613A pdb=" N LYS C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.660A pdb=" N ALA C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.470A pdb=" N THR C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 139 through 156 removed outlier: 3.825A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.725A pdb=" N ASP C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.531A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.640A pdb=" N ALA D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.788A pdb=" N ILE D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 removed outlier: 3.779A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 158 removed outlier: 3.924A pdb=" N LEU D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 169 removed outlier: 3.610A pdb=" N ILE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 181 removed outlier: 3.869A pdb=" N GLU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 removed outlier: 3.966A pdb=" N ASP E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.558A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 removed outlier: 4.414A pdb=" N MET E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 83 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 105 through 106 No H-bonds generated for 'chain 'E' and resid 105 through 106' Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 139 through 158 removed outlier: 4.644A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.595A pdb=" N ILE E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 170 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 181 removed outlier: 3.565A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.623A pdb=" N LEU F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 25' Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.515A pdb=" N ALA F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.953A pdb=" N MET F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.800A pdb=" N GLY F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.836A pdb=" N LEU F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 168 removed outlier: 3.547A pdb=" N ASP F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 181 removed outlier: 3.696A pdb=" N GLU F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 36 through 54 removed outlier: 3.551A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 76 through 81 Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 139 through 158 removed outlier: 4.060A pdb=" N LEU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG G 146 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.700A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 181 removed outlier: 3.788A pdb=" N GLU G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.532A pdb=" N LEU H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 20 through 24' Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.525A pdb=" N ALA H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 81 removed outlier: 4.007A pdb=" N MET H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 removed outlier: 3.713A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 removed outlier: 3.940A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 168 removed outlier: 3.503A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 removed outlier: 4.032A pdb=" N GLU H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 26 Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.511A pdb=" N ALA I 40 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.759A pdb=" N ALA I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'I' and resid 139 through 149 removed outlier: 3.766A pdb=" N LEU I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 removed outlier: 4.393A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.590A pdb=" N GLU I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 181 removed outlier: 3.724A pdb=" N GLU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.597A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 3.710A pdb=" N ILE J 76 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 Processing helix chain 'J' and resid 139 through 153 removed outlier: 4.178A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 163 through 169 removed outlier: 3.651A pdb=" N ASP J 167 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 181 removed outlier: 3.847A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 36 through 53 removed outlier: 3.899A pdb=" N ALA K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 75 Processing helix chain 'K' and resid 76 through 83 removed outlier: 3.874A pdb=" N GLN K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 83 " --> pdb=" O THR K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 139 through 158 removed outlier: 4.850A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA K 154 " --> pdb=" O ASN K 150 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 169 removed outlier: 3.586A pdb=" N ASP K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 181 Processing helix chain 'L' and resid 20 through 25 Processing helix chain 'L' and resid 38 through 54 removed outlier: 3.697A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 removed outlier: 3.595A pdb=" N ILE L 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.989A pdb=" N ILE L 83 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 105 Processing helix chain 'L' and resid 141 through 151 removed outlier: 3.679A pdb=" N ARG L 146 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 157 Processing helix chain 'L' and resid 161 through 169 removed outlier: 3.715A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP L 169 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 181 removed outlier: 3.808A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 39 through 54 removed outlier: 3.900A pdb=" N SER M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN M 46 " --> pdb=" O SER M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 75 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.592A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 103 Processing helix chain 'M' and resid 139 through 157 removed outlier: 3.530A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 145 " --> pdb=" O ARG M 141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M 146 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M 156 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.538A pdb=" N GLU M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 removed outlier: 4.003A pdb=" N GLU M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 36 through 52 removed outlier: 3.819A pdb=" N ASN N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 76 through 83 Processing helix chain 'N' and resid 98 through 105 Processing helix chain 'N' and resid 139 through 149 removed outlier: 3.698A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU N 145 " --> pdb=" O ARG N 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 157 Processing helix chain 'N' and resid 160 through 170 Processing helix chain 'N' and resid 175 through 181 removed outlier: 3.503A pdb=" N ALA N 179 " --> pdb=" O SER N 175 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU N 181 " --> pdb=" O GLU N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 90 removed outlier: 6.423A pdb=" N THR A 89 " --> pdb=" O TYR A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.299A pdb=" N THR B 89 " --> pdb=" O TYR B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.453A pdb=" N THR C 89 " --> pdb=" O TYR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'E' and resid 89 through 90 removed outlier: 6.462A pdb=" N THR E 89 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 89 through 90 removed outlier: 6.611A pdb=" N THR F 89 " --> pdb=" O TYR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AA8, first strand: chain 'G' and resid 89 through 90 removed outlier: 6.477A pdb=" N THR G 89 " --> pdb=" O TYR G 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AB1, first strand: chain 'H' and resid 89 through 90 removed outlier: 6.734A pdb=" N THR H 89 " --> pdb=" O TYR H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AB3, first strand: chain 'I' and resid 89 through 90 removed outlier: 6.771A pdb=" N THR I 89 " --> pdb=" O TYR I 112 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS I 187 " --> pdb=" O ARG I 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA I 113 " --> pdb=" O LYS I 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 89 through 90 removed outlier: 6.881A pdb=" N THR J 89 " --> pdb=" O TYR J 112 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 187 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA J 113 " --> pdb=" O LYS J 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=AB6, first strand: chain 'K' and resid 89 through 90 removed outlier: 6.688A pdb=" N THR K 89 " --> pdb=" O TYR K 112 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 113 " --> pdb=" O LYS K 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 89 through 90 removed outlier: 6.608A pdb=" N THR L 89 " --> pdb=" O TYR L 112 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS L 187 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 113 " --> pdb=" O LYS L 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 89 through 90 removed outlier: 6.951A pdb=" N THR M 89 " --> pdb=" O TYR M 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 89 through 90 removed outlier: 6.715A pdb=" N THR N 89 " --> pdb=" O TYR N 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 434 hydrogen bonds defined for protein. 1191 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: 10.75 Time building geometry restraints manager: 26.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17081 1.03 - 1.23: 1137 1.23 - 1.43: 5572 1.43 - 1.63: 10083 1.63 - 1.83: 182 Bond restraints: 34055 Sorted by residual: bond pdb=" C ARG N 166 " pdb=" O ARG N 166 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.17e-02 7.31e+03 3.50e+01 bond pdb=" N ARG N 170 " pdb=" CA ARG N 170 " ideal model delta sigma weight residual 1.452 1.509 -0.057 1.22e-02 6.72e+03 2.17e+01 bond pdb=" CA ALA M 105 " pdb=" CB ALA M 105 " ideal model delta sigma weight residual 1.527 1.495 0.033 7.60e-03 1.73e+04 1.83e+01 bond pdb=" C ILE M 28 " pdb=" O ILE M 28 " ideal model delta sigma weight residual 1.234 1.194 0.041 1.11e-02 8.12e+03 1.35e+01 bond pdb=" C ALA M 100 " pdb=" O ALA M 100 " ideal model delta sigma weight residual 1.235 1.279 -0.044 1.26e-02 6.30e+03 1.23e+01 ... (remaining 34050 not shown) Histogram of bond angle deviations from ideal: 65.04 - 79.94: 34 79.94 - 94.85: 27 94.85 - 109.75: 26809 109.75 - 124.65: 33870 124.65 - 139.55: 1066 Bond angle restraints: 61806 Sorted by residual: angle pdb=" C ASN J 116 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 124.67 74.53 50.15 3.00e+00 1.11e-01 2.79e+02 angle pdb=" CA SER J 117 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 114.38 65.04 49.33 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C PHE J 82 " pdb=" CA PHE J 82 " pdb=" HA PHE J 82 " ideal model delta sigma weight residual 109.00 68.21 40.79 3.00e+00 1.11e-01 1.85e+02 angle pdb=" N ASP J 37 " pdb=" CA ASP J 37 " pdb=" HA ASP J 37 " ideal model delta sigma weight residual 110.00 69.38 40.62 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C ASP J 26 " pdb=" CA ASP J 26 " pdb=" HA ASP J 26 " ideal model delta sigma weight residual 109.00 68.83 40.17 3.00e+00 1.11e-01 1.79e+02 ... (remaining 61801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 13627 18.15 - 36.30: 1655 36.30 - 54.46: 442 54.46 - 72.61: 86 72.61 - 90.76: 21 Dihedral angle restraints: 15831 sinusoidal: 8877 harmonic: 6954 Sorted by residual: dihedral pdb=" CA SER F 97 " pdb=" C SER F 97 " pdb=" N MET F 98 " pdb=" CA MET F 98 " ideal model delta harmonic sigma weight residual 180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE M 63 " pdb=" C ILE M 63 " pdb=" N ASN M 64 " pdb=" CA ASN M 64 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ILE I 63 " pdb=" C ILE I 63 " pdb=" N ASN I 64 " pdb=" CA ASN I 64 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 15828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 2703 0.366 - 0.732: 6 0.732 - 1.098: 0 1.098 - 1.464: 3 1.464 - 1.830: 4 Chirality restraints: 2716 Sorted by residual: chirality pdb=" CG LEU F 31 " pdb=" CB LEU F 31 " pdb=" CD1 LEU F 31 " pdb=" CD2 LEU F 31 " both_signs ideal model delta sigma weight residual False -2.59 -0.76 -1.83 2.00e-01 2.50e+01 8.38e+01 chirality pdb=" CG LEU F 103 " pdb=" CB LEU F 103 " pdb=" CD1 LEU F 103 " pdb=" CD2 LEU F 103 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.81e+01 chirality pdb=" CG LEU M 50 " pdb=" CB LEU M 50 " pdb=" CD1 LEU M 50 " pdb=" CD2 LEU M 50 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 ... (remaining 2713 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN N 159 " -0.240 2.00e-02 2.50e+03 2.88e-01 1.24e+03 pdb=" CD GLN N 159 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN N 159 " 0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN N 159 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN N 159 " 0.433 2.00e-02 2.50e+03 pdb="HE22 GLN N 159 " -0.447 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 81 " 0.092 2.00e-02 2.50e+03 9.49e-02 1.35e+02 pdb=" CD GLN A 81 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN A 81 " -0.082 2.00e-02 2.50e+03 pdb=" NE2 GLN A 81 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 81 " 0.142 2.00e-02 2.50e+03 pdb="HE22 GLN A 81 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 121 " -0.035 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" N HIS E 122 " 0.118 2.00e-02 2.50e+03 pdb=" CA HIS E 122 " -0.030 2.00e-02 2.50e+03 pdb=" H HIS E 122 " -0.053 2.00e-02 2.50e+03 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 0.51 - 1.33: 30 1.33 - 2.15: 1651 2.15 - 2.96: 94075 2.96 - 3.78: 122377 3.78 - 4.60: 207644 Warning: very small nonbonded interaction distances. Nonbonded interactions: 425777 Sorted by model distance: nonbonded pdb=" CD1 ILE A 83 " pdb=" HD2 PRO A 85 " model vdw 0.512 2.920 nonbonded pdb="HD11 LEU F 50 " pdb=" HE2 LYS F 57 " model vdw 0.612 2.440 nonbonded pdb="HD12 ILE A 83 " pdb=" HD2 PRO A 85 " model vdw 0.670 2.440 nonbonded pdb=" CD1 LEU F 50 " pdb=" HE2 LYS F 57 " model vdw 0.745 2.920 nonbonded pdb="HD12 LEU F 50 " pdb=" HD2 LYS F 57 " model vdw 0.825 2.440 ... (remaining 425772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA )) or resid 28 through 55 or (resid 56 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name OE2 or name H or name HA )) or (resid 57 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 58 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or \ name HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD or name CE or name H or name HA ) \ ) or resid 121 through 156 or (resid 157 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or \ name C or name O )) or (resid 159 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 161 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 162 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'B' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 55 or (resid 56 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or (resid 57 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ )) or resid 58 through 106 or (resid 107 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name OE1 or name OE2 or name H or name \ HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name SD or name CE or name H or name HA )) or r \ esid 121 through 156 or (resid 157 and (name N or name CA or name C or name O or \ name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or name \ C or name O )) or (resid 159 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 161 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 162 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or resid 57 through 83 or (re \ sid 84 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 85 through 106 or (resid 107 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2 or name H or name \ HA )) or resid 108 through 119 or (resid 120 and (name N or name CA or name C o \ r name O or name CB or name CG or name SD or name CE or name H or name HA )) or \ resid 121 through 156 or (resid 157 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2)) or (resid 158 and (name N or name CA or name \ C or name O )) or (resid 159 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 161 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2)) or (resid 162 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or resid 163 through 189)) selection = (chain 'E' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 156 or (resid 157 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 \ and (name N or name CA or name C or name O )) or (resid 159 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ )) or (resid 160 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or (resid 161 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or \ resid 163 through 186 or (resid 187 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 188 through 189)) selection = (chain 'F' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'G' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'H' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'I' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA )) or resid 58 through 106 or (res \ id 107 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or resid 108 through 119 or ( \ resid 120 and (name N or name CA or name C or name O or name CB or name CG or na \ me SD or name CE or name H or name HA )) or resid 121 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 158 and (name N or name CA or name C or name O )) or (resid 159 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name NE2)) or (resid 160 and (name N or name CA or name C or name O or name \ CB or name CG or name CD )) or (resid 161 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2)) or (resid 162 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame OE2)) or resid 163 through 189)) selection = (chain 'J' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 189)) selection = (chain 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'L' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) selection = (chain 'M' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 85 through \ 119 or (resid 120 and (name N or name CA or name C or name O or name CB or name \ CG or name SD or name CE or name H or name HA )) or resid 121 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 141 through 156 or (resid 157 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 158 and (name N or name C \ A or name C or name O )) or (resid 159 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 160 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD )) or (re \ sid 161 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name OE2)) or resid 163 through 186 \ or (resid 187 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 188 through 189)) selection = (chain 'N' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 20 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA )) or resid 28 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name H or name HA )) or (resid 57 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z or name H or name HA )) or resid 58 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 108 through 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD or name CE or nam \ e H or name HA )) or resid 121 through 156 or (resid 157 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 158 and (name \ N or name CA or name C or name O )) or (resid 159 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (res \ id 160 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 163 \ through 189)) } 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: 0.390 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: 0.500 Extract box with map and model: 3.600 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 97.050 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.011 0.077 16960 Z= 0.692 Angle : 1.206 18.600 22854 Z= 0.694 Chirality : 0.101 1.830 2716 Planarity : 0.006 0.061 2926 Dihedral : 15.697 90.760 6418 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 1.49 % Allowed : 17.69 % Favored : 80.81 % Rotamer: Outliers : 2.30 % Allowed : 9.93 % Favored : 87.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.16), residues: 2142 helix: -3.75 (0.12), residues: 720 sheet: -4.08 (0.22), residues: 239 loop : -3.02 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS I 122 PHE 0.024 0.003 PHE D 49 TYR 0.035 0.002 TYR I 182 ARG 0.008 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 691 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 650 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 28 ILE cc_start: 0.8949 (mt) cc_final: 0.8701 (mm) REVERT: A 177 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 178 GLU cc_start: 0.8021 (pt0) cc_final: 0.7536 (pt0) REVERT: C 108 LYS cc_start: 0.7479 (pttt) cc_final: 0.7028 (tttp) REVERT: C 122 HIS cc_start: 0.7864 (t70) cc_final: 0.7315 (t-90) REVERT: C 165 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8805 (tm-30) REVERT: C 170 ARG cc_start: 0.7518 (ttm110) cc_final: 0.6922 (ttt90) REVERT: C 173 PHE cc_start: 0.7991 (m-10) cc_final: 0.7171 (m-10) REVERT: D 28 ILE cc_start: 0.8700 (mt) cc_final: 0.8470 (mm) REVERT: D 108 LYS cc_start: 0.7930 (pttp) cc_final: 0.7253 (tttp) REVERT: D 118 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 173 PHE cc_start: 0.7978 (m-80) cc_final: 0.7522 (m-80) REVERT: E 58 GLU cc_start: 0.8400 (pp20) cc_final: 0.7919 (pm20) REVERT: E 163 VAL cc_start: 0.7881 (m) cc_final: 0.6820 (p) REVERT: E 165 GLU cc_start: 0.8648 (tp30) cc_final: 0.8334 (mt-10) REVERT: E 167 ASP cc_start: 0.7853 (p0) cc_final: 0.7619 (p0) REVERT: E 169 ASP cc_start: 0.7435 (t70) cc_final: 0.7183 (p0) REVERT: F 108 LYS cc_start: 0.7634 (ptpp) cc_final: 0.7297 (ptmm) REVERT: F 173 PHE cc_start: 0.7998 (m-80) cc_final: 0.7473 (m-80) REVERT: H 58 GLU cc_start: 0.7756 (pm20) cc_final: 0.7551 (pm20) REVERT: H 81 GLN cc_start: 0.7721 (tp40) cc_final: 0.7465 (tm-30) REVERT: H 101 PHE cc_start: 0.8344 (t80) cc_final: 0.8118 (t80) REVERT: H 165 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7237 (tp30) REVERT: I 58 GLU cc_start: 0.7107 (tp30) cc_final: 0.6528 (tp30) REVERT: I 162 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6662 (tm-30) REVERT: I 173 PHE cc_start: 0.7043 (m-80) cc_final: 0.6632 (m-80) REVERT: J 143 LEU cc_start: 0.8393 (tt) cc_final: 0.8174 (tp) REVERT: J 173 PHE cc_start: 0.7140 (m-80) cc_final: 0.6739 (m-10) REVERT: K 57 LYS cc_start: 0.8257 (mttt) cc_final: 0.8000 (mtpt) REVERT: K 162 GLU cc_start: 0.6554 (mp0) cc_final: 0.6002 (tm-30) REVERT: L 151 LYS cc_start: 0.8520 (tmtt) cc_final: 0.8270 (tptp) REVERT: L 167 ASP cc_start: 0.8722 (m-30) cc_final: 0.8176 (p0) REVERT: M 28 ILE cc_start: 0.9282 (mt) cc_final: 0.8954 (mm) REVERT: M 122 HIS cc_start: 0.7333 (t70) cc_final: 0.7133 (t70) REVERT: M 178 GLU cc_start: 0.8470 (pt0) cc_final: 0.8128 (pm20) REVERT: N 38 ASN cc_start: 0.8081 (m110) cc_final: 0.7812 (m110) REVERT: N 57 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7254 (tttt) REVERT: N 169 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7975 (p0) REVERT: N 178 GLU cc_start: 0.7972 (pt0) cc_final: 0.7636 (pm20) outliers start: 41 outliers final: 27 residues processed: 685 average time/residue: 0.7674 time to fit residues: 730.8903 Evaluate side-chains 452 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 424 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 101 PHE Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 46 GLN A 122 HIS B 41 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN D 41 ASN D 116 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 172 ASN H 41 ASN H 150 ASN I 172 ASN J 41 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN M 38 ASN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16960 Z= 0.242 Angle : 0.776 15.689 22854 Z= 0.404 Chirality : 0.093 1.705 2716 Planarity : 0.005 0.062 2926 Dihedral : 8.150 83.740 2416 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 13.45 % Favored : 86.04 % Rotamer: Outliers : 4.09 % Allowed : 19.91 % Favored : 76.00 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.16), residues: 2142 helix: -2.78 (0.14), residues: 908 sheet: -4.03 (0.21), residues: 274 loop : -3.22 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 122 PHE 0.019 0.002 PHE B 173 TYR 0.018 0.001 TYR M 20 ARG 0.003 0.001 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 556 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 483 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 28 ILE cc_start: 0.9051 (mt) cc_final: 0.8806 (mm) REVERT: B 173 PHE cc_start: 0.7236 (m-10) cc_final: 0.6972 (m-10) REVERT: C 108 LYS cc_start: 0.7638 (pttt) cc_final: 0.7257 (tttp) REVERT: C 169 ASP cc_start: 0.7700 (p0) cc_final: 0.7440 (p0) REVERT: C 170 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7075 (ttt90) REVERT: D 28 ILE cc_start: 0.8820 (mt) cc_final: 0.8582 (mm) REVERT: D 108 LYS cc_start: 0.8053 (pttp) cc_final: 0.7380 (tttp) REVERT: D 118 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7096 (mt-10) REVERT: D 173 PHE cc_start: 0.7944 (m-80) cc_final: 0.7515 (m-80) REVERT: E 165 GLU cc_start: 0.8667 (tp30) cc_final: 0.8402 (mt-10) REVERT: E 167 ASP cc_start: 0.7939 (p0) cc_final: 0.7725 (p0) REVERT: F 108 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7693 (ptmm) REVERT: G 58 GLU cc_start: 0.8430 (pm20) cc_final: 0.7736 (pm20) REVERT: H 46 GLN cc_start: 0.9151 (mt0) cc_final: 0.8912 (mt0) REVERT: H 81 GLN cc_start: 0.7768 (tp40) cc_final: 0.7391 (tm-30) REVERT: H 101 PHE cc_start: 0.8253 (t80) cc_final: 0.8044 (t80) REVERT: H 165 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7318 (tp30) REVERT: J 161 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7811 (tp) REVERT: K 57 LYS cc_start: 0.8298 (mttt) cc_final: 0.7954 (mmmt) REVERT: K 74 MET cc_start: 0.7562 (mmm) cc_final: 0.7341 (mmm) REVERT: K 162 GLU cc_start: 0.6613 (mp0) cc_final: 0.5991 (tm-30) REVERT: K 165 GLU cc_start: 0.7216 (mp0) cc_final: 0.6012 (tp30) REVERT: K 177 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: L 22 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7646 (mtt180) REVERT: L 30 MET cc_start: 0.7417 (tpt) cc_final: 0.7211 (tpt) REVERT: L 151 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8499 (tptp) REVERT: L 167 ASP cc_start: 0.8598 (m-30) cc_final: 0.8202 (p0) REVERT: L 177 GLU cc_start: 0.7868 (tm-30) cc_final: 0.6995 (tp30) REVERT: M 178 GLU cc_start: 0.8324 (pt0) cc_final: 0.7725 (pm20) REVERT: N 57 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7254 (tttm) REVERT: N 169 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7644 (p0) REVERT: N 173 PHE cc_start: 0.7225 (m-80) cc_final: 0.6789 (t80) outliers start: 73 outliers final: 47 residues processed: 526 average time/residue: 0.7081 time to fit residues: 532.7298 Evaluate side-chains 476 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 426 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 177 GLU Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN I 46 GLN I 122 HIS I 172 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16960 Z= 0.334 Angle : 0.784 16.121 22854 Z= 0.412 Chirality : 0.094 1.730 2716 Planarity : 0.005 0.059 2926 Dihedral : 7.209 82.546 2384 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.15 % Favored : 83.47 % Rotamer: Outliers : 5.33 % Allowed : 23.44 % Favored : 71.23 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.16), residues: 2142 helix: -2.45 (0.15), residues: 902 sheet: -3.95 (0.23), residues: 268 loop : -3.16 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS M 122 PHE 0.026 0.002 PHE J 173 TYR 0.018 0.001 TYR N 20 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 518 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 423 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7894 (t-90) REVERT: A 165 GLU cc_start: 0.7844 (mp0) cc_final: 0.7292 (mp0) REVERT: C 108 LYS cc_start: 0.7901 (pttt) cc_final: 0.7538 (tttp) REVERT: D 118 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7061 (mt-10) REVERT: D 173 PHE cc_start: 0.8001 (m-80) cc_final: 0.7461 (m-80) REVERT: F 108 LYS cc_start: 0.8118 (ptpp) cc_final: 0.7599 (tttp) REVERT: F 161 LEU cc_start: 0.8420 (tt) cc_final: 0.8186 (mt) REVERT: G 177 GLU cc_start: 0.7461 (pm20) cc_final: 0.7058 (pm20) REVERT: H 81 GLN cc_start: 0.7886 (tp40) cc_final: 0.7371 (tm-30) REVERT: H 118 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: H 165 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7153 (tp30) REVERT: I 162 GLU cc_start: 0.7257 (mp0) cc_final: 0.6275 (tm-30) REVERT: K 57 LYS cc_start: 0.8277 (mttt) cc_final: 0.8011 (mtpt) REVERT: K 162 GLU cc_start: 0.6614 (mp0) cc_final: 0.5882 (tm-30) REVERT: K 165 GLU cc_start: 0.7404 (mp0) cc_final: 0.7203 (mp0) REVERT: L 30 MET cc_start: 0.7538 (tpt) cc_final: 0.7216 (tpt) REVERT: L 167 ASP cc_start: 0.8661 (m-30) cc_final: 0.8299 (p0) REVERT: N 57 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7402 (tttm) REVERT: N 169 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7738 (p0) REVERT: N 173 PHE cc_start: 0.7109 (m-80) cc_final: 0.6864 (t80) REVERT: N 178 GLU cc_start: 0.8031 (pt0) cc_final: 0.7769 (pm20) outliers start: 95 outliers final: 61 residues processed: 473 average time/residue: 0.7346 time to fit residues: 495.8434 Evaluate side-chains 455 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 391 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 122 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 94 MET Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 167 ASP Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 99 optimal weight: 0.0170 chunk 21 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN H 172 ASN J 172 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16960 Z= 0.194 Angle : 0.688 15.548 22854 Z= 0.353 Chirality : 0.092 1.741 2716 Planarity : 0.005 0.060 2926 Dihedral : 6.413 70.219 2376 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.95 % Favored : 87.72 % Rotamer: Outliers : 5.05 % Allowed : 23.84 % Favored : 71.12 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.17), residues: 2142 helix: -1.95 (0.16), residues: 902 sheet: -3.56 (0.24), residues: 268 loop : -2.92 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 122 PHE 0.015 0.001 PHE I 173 TYR 0.016 0.001 TYR N 20 ARG 0.007 0.000 ARG N 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 434 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7898 (t-90) REVERT: A 165 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 108 LYS cc_start: 0.7875 (pttt) cc_final: 0.7491 (tttp) REVERT: C 169 ASP cc_start: 0.7707 (p0) cc_final: 0.7292 (p0) REVERT: D 108 LYS cc_start: 0.8160 (pttp) cc_final: 0.7534 (tttp) REVERT: D 118 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7136 (mt-10) REVERT: D 173 PHE cc_start: 0.7950 (m-80) cc_final: 0.7384 (m-80) REVERT: F 108 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7398 (tttm) REVERT: F 118 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6778 (mt-10) REVERT: H 81 GLN cc_start: 0.7793 (tp40) cc_final: 0.7354 (tm-30) REVERT: H 98 MET cc_start: 0.7544 (tpt) cc_final: 0.7302 (mmm) REVERT: H 165 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7226 (tp30) REVERT: I 162 GLU cc_start: 0.7119 (mp0) cc_final: 0.6480 (tm-30) REVERT: K 57 LYS cc_start: 0.8278 (mttt) cc_final: 0.8023 (mtpt) REVERT: K 162 GLU cc_start: 0.6570 (mp0) cc_final: 0.6011 (tm-30) REVERT: K 166 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7613 (ttp80) REVERT: L 167 ASP cc_start: 0.8654 (m-30) cc_final: 0.8300 (p0) REVERT: N 57 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7402 (tttm) REVERT: N 169 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7567 (p0) REVERT: N 173 PHE cc_start: 0.7059 (m-80) cc_final: 0.6840 (t80) REVERT: N 178 GLU cc_start: 0.7977 (pt0) cc_final: 0.7770 (pm20) outliers start: 90 outliers final: 65 residues processed: 478 average time/residue: 0.6998 time to fit residues: 485.6953 Evaluate side-chains 466 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 398 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 172 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 122 HIS Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 172 ASN I 46 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN L 159 GLN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16960 Z= 0.207 Angle : 0.679 14.081 22854 Z= 0.350 Chirality : 0.091 1.733 2716 Planarity : 0.004 0.046 2926 Dihedral : 6.150 70.241 2374 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.15 % Favored : 85.53 % Rotamer: Outliers : 4.49 % Allowed : 25.80 % Favored : 69.71 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.17), residues: 2142 helix: -1.70 (0.16), residues: 912 sheet: -3.32 (0.26), residues: 262 loop : -2.76 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 122 PHE 0.018 0.002 PHE I 173 TYR 0.017 0.001 TYR D 77 ARG 0.004 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 419 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: C 108 LYS cc_start: 0.7977 (pttt) cc_final: 0.7570 (tttp) REVERT: C 169 ASP cc_start: 0.7596 (p0) cc_final: 0.7219 (p0) REVERT: D 108 LYS cc_start: 0.8195 (pttp) cc_final: 0.7600 (tttp) REVERT: D 118 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7092 (mt-10) REVERT: D 173 PHE cc_start: 0.7934 (m-80) cc_final: 0.7455 (m-80) REVERT: F 108 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7457 (tttm) REVERT: F 167 ASP cc_start: 0.7962 (m-30) cc_final: 0.7669 (p0) REVERT: H 81 GLN cc_start: 0.7826 (tp40) cc_final: 0.7351 (tm-30) REVERT: H 98 MET cc_start: 0.7500 (tpt) cc_final: 0.7291 (mmm) REVERT: H 165 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7212 (tp30) REVERT: I 53 GLU cc_start: 0.6817 (tp30) cc_final: 0.6210 (tm-30) REVERT: K 57 LYS cc_start: 0.8230 (mttt) cc_final: 0.8008 (mtpt) REVERT: L 30 MET cc_start: 0.7493 (tpt) cc_final: 0.7093 (tpt) REVERT: L 167 ASP cc_start: 0.8672 (m-30) cc_final: 0.8332 (p0) REVERT: N 169 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7609 (p0) outliers start: 80 outliers final: 62 residues processed: 461 average time/residue: 0.6949 time to fit residues: 463.7915 Evaluate side-chains 453 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 389 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 0.0570 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.0020 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 2.8112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16960 Z= 0.173 Angle : 0.651 14.240 22854 Z= 0.332 Chirality : 0.092 1.741 2716 Planarity : 0.004 0.042 2926 Dihedral : 5.746 66.634 2371 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.50 % Favored : 89.17 % Rotamer: Outliers : 4.04 % Allowed : 26.70 % Favored : 69.27 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.18), residues: 2142 helix: -1.35 (0.17), residues: 896 sheet: -3.00 (0.27), residues: 262 loop : -2.54 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 122 PHE 0.012 0.001 PHE A 82 TYR 0.014 0.001 TYR N 77 ARG 0.003 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 501 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 429 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: C 108 LYS cc_start: 0.7949 (pttt) cc_final: 0.7521 (tttm) REVERT: C 169 ASP cc_start: 0.7533 (p0) cc_final: 0.7219 (p0) REVERT: D 108 LYS cc_start: 0.8152 (pttp) cc_final: 0.7560 (tttp) REVERT: D 118 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 173 PHE cc_start: 0.7973 (m-80) cc_final: 0.6910 (m-80) REVERT: F 108 LYS cc_start: 0.8031 (ptpp) cc_final: 0.7432 (tttm) REVERT: H 81 GLN cc_start: 0.7830 (tp40) cc_final: 0.7522 (tm-30) REVERT: H 165 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7238 (tp30) REVERT: K 57 LYS cc_start: 0.8241 (mttt) cc_final: 0.8027 (mtpt) REVERT: K 166 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7666 (ttm110) REVERT: L 30 MET cc_start: 0.7465 (tpt) cc_final: 0.7123 (tpt) REVERT: L 80 MET cc_start: 0.8281 (mmm) cc_final: 0.7959 (mmm) REVERT: N 22 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8147 (mtt180) REVERT: N 57 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7727 (tttm) REVERT: N 169 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7597 (p0) REVERT: N 189 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7204 (pp) outliers start: 72 outliers final: 58 residues processed: 465 average time/residue: 0.6787 time to fit residues: 462.6569 Evaluate side-chains 456 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 395 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 0.0060 chunk 113 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16960 Z= 0.230 Angle : 0.687 14.456 22854 Z= 0.352 Chirality : 0.092 1.735 2716 Planarity : 0.004 0.040 2926 Dihedral : 5.732 63.071 2371 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.68 % Favored : 86.04 % Rotamer: Outliers : 4.60 % Allowed : 26.98 % Favored : 68.42 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.18), residues: 2142 helix: -1.48 (0.17), residues: 920 sheet: -2.97 (0.28), residues: 262 loop : -2.56 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 122 PHE 0.014 0.002 PHE L 49 TYR 0.014 0.001 TYR N 20 ARG 0.003 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 402 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: C 108 LYS cc_start: 0.8023 (pttt) cc_final: 0.7665 (tttp) REVERT: C 169 ASP cc_start: 0.7575 (p0) cc_final: 0.7248 (p0) REVERT: D 108 LYS cc_start: 0.8202 (pttp) cc_final: 0.7660 (tttp) REVERT: D 118 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7114 (mt-10) REVERT: D 173 PHE cc_start: 0.7510 (m-80) cc_final: 0.6853 (m-80) REVERT: F 108 LYS cc_start: 0.8109 (ptpp) cc_final: 0.7609 (tttp) REVERT: F 165 GLU cc_start: 0.7965 (mp0) cc_final: 0.7735 (mp0) REVERT: H 81 GLN cc_start: 0.7928 (tp40) cc_final: 0.7573 (tm-30) REVERT: H 165 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7182 (tp30) REVERT: K 57 LYS cc_start: 0.8274 (mttt) cc_final: 0.8053 (mtpt) REVERT: L 167 ASP cc_start: 0.8612 (m-30) cc_final: 0.8271 (p0) REVERT: N 22 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8214 (mtt180) REVERT: N 57 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7669 (tttm) REVERT: N 169 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7496 (p0) REVERT: N 189 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (pp) outliers start: 82 outliers final: 67 residues processed: 446 average time/residue: 0.6662 time to fit residues: 431.6407 Evaluate side-chains 457 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 387 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16960 Z= 0.183 Angle : 0.655 14.390 22854 Z= 0.333 Chirality : 0.092 1.742 2716 Planarity : 0.004 0.040 2926 Dihedral : 5.613 66.460 2371 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % Rotamer: Outliers : 3.87 % Allowed : 27.93 % Favored : 68.20 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 2142 helix: -1.25 (0.17), residues: 920 sheet: -2.75 (0.28), residues: 262 loop : -2.41 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 122 PHE 0.015 0.001 PHE L 49 TYR 0.013 0.001 TYR N 77 ARG 0.002 0.000 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 418 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: C 108 LYS cc_start: 0.7989 (pttt) cc_final: 0.7528 (tttp) REVERT: C 169 ASP cc_start: 0.7548 (p0) cc_final: 0.7277 (p0) REVERT: D 108 LYS cc_start: 0.8184 (pttp) cc_final: 0.7634 (tttp) REVERT: D 118 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7208 (mt-10) REVERT: D 165 GLU cc_start: 0.7719 (pm20) cc_final: 0.7384 (pm20) REVERT: D 173 PHE cc_start: 0.7516 (m-80) cc_final: 0.6865 (m-80) REVERT: E 19 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7092 (tp) REVERT: E 120 MET cc_start: 0.8290 (ptt) cc_final: 0.7928 (ptt) REVERT: E 182 TYR cc_start: 0.7904 (m-80) cc_final: 0.7639 (m-80) REVERT: F 108 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7558 (tttp) REVERT: F 120 MET cc_start: 0.7488 (ttt) cc_final: 0.7181 (ttt) REVERT: F 165 GLU cc_start: 0.8042 (mp0) cc_final: 0.7805 (mp0) REVERT: H 81 GLN cc_start: 0.7967 (tp40) cc_final: 0.7596 (tm-30) REVERT: H 165 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7195 (tp30) REVERT: H 166 ARG cc_start: 0.8130 (ptm-80) cc_final: 0.7671 (ptm160) REVERT: K 30 MET cc_start: 0.7750 (tpt) cc_final: 0.7301 (tpt) REVERT: K 57 LYS cc_start: 0.8279 (mttt) cc_final: 0.8067 (mtpt) REVERT: K 162 GLU cc_start: 0.6827 (mp0) cc_final: 0.6234 (tm-30) REVERT: L 117 SER cc_start: 0.8892 (m) cc_final: 0.8602 (p) REVERT: N 22 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8221 (mtt180) REVERT: N 169 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7428 (p0) REVERT: N 189 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7195 (pp) outliers start: 69 outliers final: 57 residues processed: 455 average time/residue: 0.6876 time to fit residues: 459.9621 Evaluate side-chains 452 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 391 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 147 ASP Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16960 Z= 0.271 Angle : 0.716 14.502 22854 Z= 0.366 Chirality : 0.092 1.734 2716 Planarity : 0.004 0.039 2926 Dihedral : 5.570 47.551 2368 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.71 % Favored : 85.11 % Rotamer: Outliers : 4.43 % Allowed : 28.21 % Favored : 67.36 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.17), residues: 2142 helix: -1.52 (0.16), residues: 928 sheet: -2.84 (0.28), residues: 262 loop : -2.46 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 122 PHE 0.017 0.002 PHE I 173 TYR 0.014 0.001 TYR L 20 ARG 0.007 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 397 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: C 169 ASP cc_start: 0.7599 (p0) cc_final: 0.7324 (p0) REVERT: D 108 LYS cc_start: 0.8273 (pttp) cc_final: 0.7828 (tttp) REVERT: D 118 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7176 (mt-10) REVERT: D 173 PHE cc_start: 0.7541 (m-80) cc_final: 0.7006 (m-80) REVERT: E 19 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7124 (tp) REVERT: E 120 MET cc_start: 0.8301 (ptt) cc_final: 0.7898 (ptt) REVERT: E 182 TYR cc_start: 0.7998 (m-80) cc_final: 0.7749 (m-80) REVERT: F 108 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7687 (tttp) REVERT: F 120 MET cc_start: 0.7508 (ttt) cc_final: 0.7203 (ttt) REVERT: F 165 GLU cc_start: 0.8073 (mp0) cc_final: 0.7868 (mp0) REVERT: H 81 GLN cc_start: 0.8053 (tp40) cc_final: 0.7634 (tm-30) REVERT: L 30 MET cc_start: 0.7501 (tpt) cc_final: 0.7154 (tpt) REVERT: N 57 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7715 (tttm) REVERT: N 169 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (p0) REVERT: N 189 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7209 (pp) outliers start: 79 outliers final: 66 residues processed: 439 average time/residue: 0.6829 time to fit residues: 433.9776 Evaluate side-chains 462 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 392 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 116 ASN Chi-restraints excluded: chain K residue 147 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 147 ASP Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 0.1980 chunk 132 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16960 Z= 0.164 Angle : 0.665 14.255 22854 Z= 0.334 Chirality : 0.092 1.746 2716 Planarity : 0.004 0.043 2926 Dihedral : 5.313 50.122 2368 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.57 % Favored : 90.24 % Rotamer: Outliers : 3.03 % Allowed : 29.95 % Favored : 67.02 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 2142 helix: -1.11 (0.17), residues: 924 sheet: -2.50 (0.30), residues: 262 loop : -2.27 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 122 PHE 0.019 0.001 PHE L 49 TYR 0.013 0.001 TYR N 77 ARG 0.005 0.000 ARG C 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue MET 120 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 474 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 420 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: B 112 TYR cc_start: 0.8150 (m-80) cc_final: 0.7929 (m-80) REVERT: C 50 LEU cc_start: 0.8879 (tt) cc_final: 0.8584 (mt) REVERT: C 122 HIS cc_start: 0.8142 (t70) cc_final: 0.7494 (t-90) REVERT: C 169 ASP cc_start: 0.7532 (p0) cc_final: 0.7118 (p0) REVERT: D 108 LYS cc_start: 0.8149 (pttp) cc_final: 0.7708 (tttp) REVERT: D 118 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 141 ARG cc_start: 0.7754 (tmm-80) cc_final: 0.7345 (tmm-80) REVERT: D 165 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: D 173 PHE cc_start: 0.7517 (m-80) cc_final: 0.7037 (m-80) REVERT: E 120 MET cc_start: 0.8295 (ptt) cc_final: 0.7985 (ptt) REVERT: E 182 TYR cc_start: 0.7909 (m-80) cc_final: 0.7669 (m-80) REVERT: F 108 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7527 (tttp) REVERT: F 120 MET cc_start: 0.7477 (ttt) cc_final: 0.7165 (ttt) REVERT: F 165 GLU cc_start: 0.8087 (mp0) cc_final: 0.7876 (mp0) REVERT: H 81 GLN cc_start: 0.7993 (tp40) cc_final: 0.7614 (tm-30) REVERT: H 165 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7236 (tp30) REVERT: I 120 MET cc_start: 0.7551 (mmm) cc_final: 0.7274 (mmm) REVERT: K 30 MET cc_start: 0.7727 (tpt) cc_final: 0.7423 (tpt) REVERT: M 22 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8160 (ttt180) REVERT: N 22 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8281 (mtt180) REVERT: N 169 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (p0) REVERT: N 189 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7202 (pp) outliers start: 54 outliers final: 44 residues processed: 449 average time/residue: 0.6883 time to fit residues: 448.8754 Evaluate side-chains 452 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 404 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 156 ARG Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 169 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104392 restraints weight = 125099.030| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 5.24 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16960 Z= 0.234 Angle : 0.696 14.465 22854 Z= 0.353 Chirality : 0.092 1.737 2716 Planarity : 0.004 0.038 2926 Dihedral : 5.371 47.905 2368 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.35 % Favored : 86.46 % Rotamer: Outliers : 3.14 % Allowed : 29.78 % Favored : 67.08 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 2142 helix: -1.30 (0.17), residues: 936 sheet: -2.62 (0.29), residues: 262 loop : -2.29 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 122 PHE 0.017 0.002 PHE I 173 TYR 0.014 0.001 TYR L 20 ARG 0.005 0.000 ARG C 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8537.43 seconds wall clock time: 150 minutes 17.69 seconds (9017.69 seconds total)