Starting phenix.real_space_refine on Wed May 6 02:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ufn_64113/05_2026/9ufn_64113.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 21888 2.51 5 N 5844 2.21 5 O 6738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34614 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "B" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "C" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Chain: "E" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "G" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "H" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Chain: "I" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "J" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "K" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "L" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Chain: "M" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "N" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "O" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "P" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Chain: "Q" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "R" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "S" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "T" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Chain: "U" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "V" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1295 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "W" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1294 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain breaks: 1 Chain: "X" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 5 Time building chain proxies: 7.75, per 1000 atoms: 0.22 Number of scatterers: 34614 At special positions: 0 Unit cell: (119.574, 119.574, 219.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6738 8.00 N 5844 7.00 C 21888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8196 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 78 sheets defined 23.6% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR A 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 34 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL C 181 " --> pdb=" O TRP C 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 259 Processing helix chain 'D' and resid 263 through 283 removed outlier: 3.860A pdb=" N LYS D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR E 33 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.780A pdb=" N TYR E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.800A pdb=" N VAL G 181 " --> pdb=" O TRP G 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.622A pdb=" N VAL G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.690A pdb=" N TYR H 234 " --> pdb=" O ASN H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 259 Processing helix chain 'H' and resid 263 through 283 removed outlier: 3.860A pdb=" N LYS H 269 " --> pdb=" O GLU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR H 360 " --> pdb=" O ARG H 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR I 33 " --> pdb=" O GLN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 93 Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.780A pdb=" N TYR I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 34 Processing helix chain 'J' and resid 79 through 94 removed outlier: 3.586A pdb=" N ALA J 92 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 11 Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL K 181 " --> pdb=" O TRP K 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 182 " --> pdb=" O VAL K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 83 removed outlier: 3.503A pdb=" N LEU L 77 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR L 234 " --> pdb=" O ASN L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 259 Processing helix chain 'L' and resid 263 through 283 removed outlier: 3.860A pdb=" N LYS L 269 " --> pdb=" O GLU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 removed outlier: 4.665A pdb=" N TYR L 360 " --> pdb=" O ARG L 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 9 Processing helix chain 'M' and resid 29 through 34 removed outlier: 3.646A pdb=" N THR M 33 " --> pdb=" O GLN M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 93 Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.779A pdb=" N TYR M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE N 10 " --> pdb=" O VAL N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 34 Processing helix chain 'N' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA N 92 " --> pdb=" O TRP N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 11 Processing helix chain 'O' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL O 181 " --> pdb=" O TRP O 177 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN O 182 " --> pdb=" O VAL O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL O 195 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 234 removed outlier: 3.690A pdb=" N TYR P 234 " --> pdb=" O ASN P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 259 Processing helix chain 'P' and resid 263 through 283 removed outlier: 3.860A pdb=" N LYS P 269 " --> pdb=" O GLU P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR P 360 " --> pdb=" O ARG P 356 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.647A pdb=" N THR Q 33 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 93 Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.778A pdb=" N TYR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE R 10 " --> pdb=" O VAL R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 34 Processing helix chain 'R' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA R 92 " --> pdb=" O TRP R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 Processing helix chain 'S' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL S 181 " --> pdb=" O TRP S 177 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN S 182 " --> pdb=" O VAL S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 196 removed outlier: 3.621A pdb=" N VAL S 195 " --> pdb=" O LEU S 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 83 removed outlier: 3.503A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 234 removed outlier: 3.691A pdb=" N TYR T 234 " --> pdb=" O ASN T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 259 Processing helix chain 'T' and resid 263 through 283 removed outlier: 3.859A pdb=" N LYS T 269 " --> pdb=" O GLU T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 355 through 360 removed outlier: 4.665A pdb=" N TYR T 360 " --> pdb=" O ARG T 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 9 Processing helix chain 'U' and resid 29 through 34 removed outlier: 3.648A pdb=" N THR U 33 " --> pdb=" O GLN U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 Processing helix chain 'U' and resid 103 through 108 removed outlier: 3.778A pdb=" N TYR U 107 " --> pdb=" O LYS U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 10 removed outlier: 3.802A pdb=" N PHE V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 34 Processing helix chain 'V' and resid 79 through 94 removed outlier: 3.587A pdb=" N ALA V 92 " --> pdb=" O TRP V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 3.774A pdb=" N TYR V 107 " --> pdb=" O LYS V 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 11 Processing helix chain 'W' and resid 168 through 182 removed outlier: 3.799A pdb=" N VAL W 181 " --> pdb=" O TRP W 177 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN W 182 " --> pdb=" O VAL W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 196 removed outlier: 3.622A pdb=" N VAL W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 83 removed outlier: 3.502A pdb=" N LEU X 77 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 215 through 234 removed outlier: 3.690A pdb=" N TYR X 234 " --> pdb=" O ASN X 230 " (cutoff:3.500A) Processing helix chain 'X' and resid 242 through 259 Processing helix chain 'X' and resid 263 through 283 removed outlier: 3.859A pdb=" N LYS X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 355 through 360 removed outlier: 4.664A pdb=" N TYR X 360 " --> pdb=" O ARG X 356 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN A 22 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 111 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 161 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU A 154 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL A 137 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 156 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE A 45 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG A 64 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 47 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG B 114 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 109 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 131 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 115 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS B 125 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR B 156 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 38 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 74 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS B 36 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG B 114 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 109 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 131 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 115 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS B 125 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 161 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=7, first strand: chain 'C' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE C 199 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 217 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 201 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET C 215 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 203 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA C 213 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA C 245 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 159 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 127 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE C 199 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 217 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 201 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET C 215 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 203 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA C 213 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG C 134 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG C 153 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 136 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR D 34 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU D 128 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 36 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 125 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=12, first strand: chain 'D' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG D 142 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG D 349 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE D 316 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN E 22 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 111 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 36 through 39 removed outlier: 7.907A pdb=" N GLU E 154 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL E 137 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR E 156 " --> pdb=" O THR E 135 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 45 through 52 removed outlier: 7.410A pdb=" N ILE E 45 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG E 64 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU E 47 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG F 114 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS F 109 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY F 131 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 115 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 125 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR F 156 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 38 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET F 74 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N CYS F 36 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG F 114 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS F 109 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY F 131 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 115 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 125 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 161 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 48 through 52 Processing sheet with id=20, first strand: chain 'G' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE G 199 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR G 217 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL G 201 " --> pdb=" O MET G 215 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET G 215 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU G 203 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA G 213 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA G 245 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 159 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER G 127 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE G 199 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR G 217 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL G 201 " --> pdb=" O MET G 215 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET G 215 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU G 203 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA G 213 " --> pdb=" O LEU G 203 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 134 through 140 removed outlier: 7.800A pdb=" N ARG G 134 " --> pdb=" O ARG G 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG G 153 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER G 136 " --> pdb=" O THR G 151 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.161A pdb=" N TYR H 34 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU H 128 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA H 36 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 125 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=25, first strand: chain 'H' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG H 142 " --> pdb=" O GLY H 198 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG H 349 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE H 316 " --> pdb=" O ARG H 349 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 21 through 25 removed outlier: 3.829A pdb=" N GLN I 22 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 111 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR I 161 " --> pdb=" O LYS I 130 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 36 through 39 removed outlier: 7.907A pdb=" N GLU I 154 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL I 137 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR I 156 " --> pdb=" O THR I 135 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'I' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE I 45 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG I 64 " --> pdb=" O ILE I 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU I 47 " --> pdb=" O GLY I 62 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG J 114 " --> pdb=" O GLN J 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS J 109 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY J 131 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 115 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS J 125 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR J 156 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA J 38 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET J 74 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS J 36 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG J 114 " --> pdb=" O GLN J 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS J 109 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY J 131 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 115 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS J 125 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR J 161 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 48 through 52 Processing sheet with id=33, first strand: chain 'K' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE K 199 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR K 217 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL K 201 " --> pdb=" O MET K 215 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET K 215 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU K 203 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA K 213 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA K 245 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL K 159 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER K 127 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE K 199 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR K 217 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL K 201 " --> pdb=" O MET K 215 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET K 215 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU K 203 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA K 213 " --> pdb=" O LEU K 203 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'K' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG K 134 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG K 153 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER K 136 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR L 34 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU L 128 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA L 36 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 125 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=38, first strand: chain 'L' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG L 142 " --> pdb=" O GLY L 198 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'L' and resid 204 through 208 removed outlier: 6.064A pdb=" N ARG L 349 " --> pdb=" O ILE L 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE L 316 " --> pdb=" O ARG L 349 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 21 through 25 removed outlier: 3.829A pdb=" N GLN M 22 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA M 111 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR M 161 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'M' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU M 154 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL M 137 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR M 156 " --> pdb=" O THR M 135 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'M' and resid 45 through 52 removed outlier: 7.410A pdb=" N ILE M 45 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG M 64 " --> pdb=" O ILE M 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU M 47 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG N 114 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS N 109 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY N 131 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN N 115 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS N 125 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR N 156 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA N 38 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET N 74 " --> pdb=" O CYS N 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS N 36 " --> pdb=" O MET N 74 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'N' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG N 114 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS N 109 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY N 131 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN N 115 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS N 125 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR N 161 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 48 through 52 Processing sheet with id=46, first strand: chain 'O' and resid 23 through 26 removed outlier: 5.013A pdb=" N ILE O 199 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR O 217 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL O 201 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET O 215 " --> pdb=" O VAL O 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU O 203 " --> pdb=" O ALA O 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA O 213 " --> pdb=" O LEU O 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA O 245 " --> pdb=" O PRO O 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL O 159 " --> pdb=" O LYS O 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER O 127 " --> pdb=" O SER O 161 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 23 through 26 removed outlier: 5.013A pdb=" N ILE O 199 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR O 217 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL O 201 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET O 215 " --> pdb=" O VAL O 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU O 203 " --> pdb=" O ALA O 213 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA O 213 " --> pdb=" O LEU O 203 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG O 134 " --> pdb=" O ARG O 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG O 153 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER O 136 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'P' and resid 34 through 37 removed outlier: 6.161A pdb=" N TYR P 34 " --> pdb=" O ASN P 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU P 128 " --> pdb=" O TYR P 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA P 36 " --> pdb=" O LEU P 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA P 125 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'P' and resid 43 through 44 Processing sheet with id=51, first strand: chain 'P' and resid 141 through 144 removed outlier: 5.357A pdb=" N ARG P 142 " --> pdb=" O GLY P 198 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'P' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG P 349 " --> pdb=" O ILE P 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE P 316 " --> pdb=" O ARG P 349 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 21 through 25 removed outlier: 3.828A pdb=" N GLN Q 22 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA Q 111 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR Q 161 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 36 through 39 removed outlier: 7.906A pdb=" N GLU Q 154 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL Q 137 " --> pdb=" O GLU Q 154 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR Q 156 " --> pdb=" O THR Q 135 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 45 through 52 removed outlier: 7.408A pdb=" N ILE Q 45 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG Q 64 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU Q 47 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'R' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG R 114 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS R 109 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY R 131 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN R 115 " --> pdb=" O LYS R 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS R 125 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR R 156 " --> pdb=" O THR R 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA R 38 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET R 74 " --> pdb=" O CYS R 36 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N CYS R 36 " --> pdb=" O MET R 74 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'R' and resid 21 through 25 removed outlier: 3.509A pdb=" N ARG R 114 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS R 109 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY R 131 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN R 115 " --> pdb=" O LYS R 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS R 125 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR R 161 " --> pdb=" O LYS R 130 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'R' and resid 48 through 52 Processing sheet with id=59, first strand: chain 'S' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE S 199 " --> pdb=" O THR S 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR S 217 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL S 201 " --> pdb=" O MET S 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET S 215 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU S 203 " --> pdb=" O ALA S 213 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA S 213 " --> pdb=" O LEU S 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA S 245 " --> pdb=" O PRO S 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL S 159 " --> pdb=" O LYS S 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER S 127 " --> pdb=" O SER S 161 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE S 199 " --> pdb=" O THR S 217 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR S 217 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL S 201 " --> pdb=" O MET S 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET S 215 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU S 203 " --> pdb=" O ALA S 213 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA S 213 " --> pdb=" O LEU S 203 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 134 through 140 removed outlier: 7.801A pdb=" N ARG S 134 " --> pdb=" O ARG S 153 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG S 153 " --> pdb=" O ARG S 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER S 136 " --> pdb=" O THR S 151 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'T' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR T 34 " --> pdb=" O ASN T 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU T 128 " --> pdb=" O TYR T 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA T 36 " --> pdb=" O LEU T 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA T 125 " --> pdb=" O ALA T 66 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'T' and resid 43 through 44 Processing sheet with id=64, first strand: chain 'T' and resid 141 through 144 removed outlier: 5.358A pdb=" N ARG T 142 " --> pdb=" O GLY T 198 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'T' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG T 349 " --> pdb=" O ILE T 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE T 316 " --> pdb=" O ARG T 349 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'U' and resid 21 through 25 removed outlier: 3.829A pdb=" N GLN U 22 " --> pdb=" O ARG U 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA U 111 " --> pdb=" O ILE U 129 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR U 161 " --> pdb=" O LYS U 130 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'U' and resid 36 through 39 removed outlier: 7.907A pdb=" N GLU U 154 " --> pdb=" O VAL U 137 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL U 137 " --> pdb=" O GLU U 154 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR U 156 " --> pdb=" O THR U 135 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'U' and resid 45 through 52 removed outlier: 7.409A pdb=" N ILE U 45 " --> pdb=" O ARG U 64 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG U 64 " --> pdb=" O ILE U 45 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU U 47 " --> pdb=" O GLY U 62 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.508A pdb=" N ARG V 114 " --> pdb=" O GLN V 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS V 109 " --> pdb=" O GLY V 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY V 131 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN V 115 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS V 125 " --> pdb=" O GLN V 115 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR V 156 " --> pdb=" O THR V 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA V 38 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET V 74 " --> pdb=" O CYS V 36 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS V 36 " --> pdb=" O MET V 74 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.508A pdb=" N ARG V 114 " --> pdb=" O GLN V 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS V 109 " --> pdb=" O GLY V 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY V 131 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN V 115 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS V 125 " --> pdb=" O GLN V 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR V 161 " --> pdb=" O LYS V 130 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 48 through 52 Processing sheet with id=72, first strand: chain 'W' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE W 199 " --> pdb=" O THR W 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR W 217 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL W 201 " --> pdb=" O MET W 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET W 215 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU W 203 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA W 213 " --> pdb=" O LEU W 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA W 245 " --> pdb=" O PRO W 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL W 159 " --> pdb=" O LYS W 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER W 127 " --> pdb=" O SER W 161 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'W' and resid 23 through 26 removed outlier: 5.014A pdb=" N ILE W 199 " --> pdb=" O THR W 217 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR W 217 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL W 201 " --> pdb=" O MET W 215 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N MET W 215 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU W 203 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA W 213 " --> pdb=" O LEU W 203 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'W' and resid 134 through 140 removed outlier: 7.800A pdb=" N ARG W 134 " --> pdb=" O ARG W 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG W 153 " --> pdb=" O ARG W 134 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER W 136 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'X' and resid 34 through 37 removed outlier: 6.160A pdb=" N TYR X 34 " --> pdb=" O ASN X 126 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU X 128 " --> pdb=" O TYR X 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA X 36 " --> pdb=" O LEU X 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA X 125 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'X' and resid 43 through 44 Processing sheet with id=77, first strand: chain 'X' and resid 141 through 144 removed outlier: 5.358A pdb=" N ARG X 142 " --> pdb=" O GLY X 198 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'X' and resid 204 through 208 removed outlier: 6.065A pdb=" N ARG X 349 " --> pdb=" O ILE X 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE X 316 " --> pdb=" O ARG X 349 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3438 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: 7.47 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11431 1.34 - 1.46: 5919 1.46 - 1.57: 17756 1.57 - 1.69: 0 1.69 - 1.80: 252 Bond restraints: 35358 Sorted by residual: bond pdb=" CA LYS J 48 " pdb=" C LYS J 48 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.25e-02 6.40e+03 4.59e+00 bond pdb=" CA LYS F 48 " pdb=" C LYS F 48 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.25e-02 6.40e+03 4.45e+00 bond pdb=" CA LYS V 48 " pdb=" C LYS V 48 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.25e-02 6.40e+03 4.44e+00 bond pdb=" CA LYS B 48 " pdb=" C LYS B 48 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.25e-02 6.40e+03 4.37e+00 bond pdb=" CA LYS N 48 " pdb=" C LYS N 48 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.25e-02 6.40e+03 4.35e+00 ... (remaining 35353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 46460 1.45 - 2.91: 1160 2.91 - 4.36: 272 4.36 - 5.82: 36 5.82 - 7.27: 24 Bond angle restraints: 47952 Sorted by residual: angle pdb=" C LYS D 276 " pdb=" N MET D 277 " pdb=" CA MET D 277 " ideal model delta sigma weight residual 121.14 113.87 7.27 1.75e+00 3.27e-01 1.73e+01 angle pdb=" C LYS H 276 " pdb=" N MET H 277 " pdb=" CA MET H 277 " ideal model delta sigma weight residual 121.14 113.88 7.26 1.75e+00 3.27e-01 1.72e+01 angle pdb=" C LYS P 276 " pdb=" N MET P 277 " pdb=" CA MET P 277 " ideal model delta sigma weight residual 121.14 113.90 7.24 1.75e+00 3.27e-01 1.71e+01 angle pdb=" C LYS L 276 " pdb=" N MET L 277 " pdb=" CA MET L 277 " ideal model delta sigma weight residual 121.14 113.91 7.23 1.75e+00 3.27e-01 1.71e+01 angle pdb=" C LYS T 276 " pdb=" N MET T 277 " pdb=" CA MET T 277 " ideal model delta sigma weight residual 121.14 113.91 7.23 1.75e+00 3.27e-01 1.71e+01 ... (remaining 47947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 19015 17.94 - 35.89: 1620 35.89 - 53.83: 281 53.83 - 71.77: 54 71.77 - 89.71: 30 Dihedral angle restraints: 21000 sinusoidal: 8352 harmonic: 12648 Sorted by residual: dihedral pdb=" CB GLU B 163 " pdb=" CG GLU B 163 " pdb=" CD GLU B 163 " pdb=" OE1 GLU B 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU V 163 " pdb=" CG GLU V 163 " pdb=" CD GLU V 163 " pdb=" OE1 GLU V 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU R 163 " pdb=" CG GLU R 163 " pdb=" CD GLU R 163 " pdb=" OE1 GLU R 163 " ideal model delta sinusoidal sigma weight residual 0.00 -89.69 89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3283 0.033 - 0.066: 1321 0.066 - 0.099: 400 0.099 - 0.132: 218 0.132 - 0.164: 22 Chirality restraints: 5244 Sorted by residual: chirality pdb=" CB ILE J 127 " pdb=" CA ILE J 127 " pdb=" CG1 ILE J 127 " pdb=" CG2 ILE J 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CB ILE F 127 " pdb=" CA ILE F 127 " pdb=" CG1 ILE F 127 " pdb=" CG2 ILE F 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE R 127 " pdb=" CA ILE R 127 " pdb=" CG1 ILE R 127 " pdb=" CG2 ILE R 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 5241 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 53 " 0.015 2.00e-02 2.50e+03 1.77e-02 5.48e+00 pdb=" CG PHE V 53 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE V 53 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE V 53 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE V 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE V 53 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE V 53 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 53 " -0.016 2.00e-02 2.50e+03 1.77e-02 5.47e+00 pdb=" CG PHE F 53 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 53 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE F 53 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE F 53 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE F 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 53 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 53 " -0.015 2.00e-02 2.50e+03 1.76e-02 5.43e+00 pdb=" CG PHE N 53 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE N 53 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE N 53 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE N 53 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE N 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 53 " 0.000 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 0.52 - 1.39: 24 1.39 - 2.27: 222 2.27 - 3.15: 29437 3.15 - 4.02: 86164 4.02 - 4.90: 160017 Warning: very small nonbonded interaction distances. Nonbonded interactions: 275864 Sorted by model distance: nonbonded pdb=" OE1 GLU I 47 " pdb=" ND2 ASN O 235 " model vdw 0.518 3.120 nonbonded pdb=" OE1 GLU A 47 " pdb=" ND2 ASN G 235 " model vdw 0.518 3.120 nonbonded pdb=" ND2 ASN C 235 " pdb=" OE1 GLU U 47 " model vdw 0.518 3.120 nonbonded pdb=" OE1 GLU M 47 " pdb=" ND2 ASN S 235 " model vdw 0.519 3.120 nonbonded pdb=" OE1 GLU E 47 " pdb=" ND2 ASN K 235 " model vdw 0.519 3.120 ... (remaining 275859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.470 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 32.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 35370 Z= 0.598 Angle : 0.596 7.274 47952 Z= 0.323 Chirality : 0.043 0.164 5244 Planarity : 0.003 0.035 6264 Dihedral : 14.069 89.714 12804 Min Nonbonded Distance : 0.518 Molprobity Statistics. All-atom Clashscore : 34.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4230 helix: 1.54 (0.18), residues: 822 sheet: -0.42 (0.14), residues: 1476 loop : -1.62 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 56 TYR 0.010 0.001 TYR H 34 PHE 0.041 0.002 PHE F 53 TRP 0.039 0.001 TRP P 209 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00410 (35358) covalent geometry : angle 0.59601 (47952) hydrogen bonds : bond 0.19913 ( 1158) hydrogen bonds : angle 8.80436 ( 3438) Misc. bond : bond 0.30717 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 975 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8999 (p90) cc_final: 0.8782 (p90) REVERT: A 132 LEU cc_start: 0.9178 (mt) cc_final: 0.8955 (mp) REVERT: B 118 ARG cc_start: 0.8498 (mmm160) cc_final: 0.7258 (ttp-170) REVERT: B 157 LEU cc_start: 0.8934 (mt) cc_final: 0.8664 (mt) REVERT: C 159 VAL cc_start: 0.9375 (t) cc_final: 0.9026 (m) REVERT: C 198 ASP cc_start: 0.8324 (t0) cc_final: 0.7907 (t0) REVERT: C 241 ASP cc_start: 0.8977 (p0) cc_final: 0.8562 (p0) REVERT: D 277 MET cc_start: 0.4323 (pmm) cc_final: 0.2322 (mmp) REVERT: D 292 VAL cc_start: 0.8876 (p) cc_final: 0.8533 (m) REVERT: D 294 MET cc_start: 0.7580 (ttm) cc_final: 0.6915 (ttt) REVERT: D 348 MET cc_start: 0.8474 (ttm) cc_final: 0.7606 (ttm) REVERT: E 103 LYS cc_start: 0.8549 (mmtp) cc_final: 0.7780 (mtmm) REVERT: E 139 GLU cc_start: 0.7821 (tp30) cc_final: 0.7473 (tp30) REVERT: E 151 GLN cc_start: 0.8596 (tt0) cc_final: 0.7913 (tt0) REVERT: F 118 ARG cc_start: 0.8623 (mmm160) cc_final: 0.7549 (tmm160) REVERT: G 125 ILE cc_start: 0.9378 (mp) cc_final: 0.9050 (mt) REVERT: G 159 VAL cc_start: 0.9510 (t) cc_final: 0.9091 (m) REVERT: G 176 ASP cc_start: 0.8643 (t70) cc_final: 0.8391 (t0) REVERT: G 215 MET cc_start: 0.8097 (ttm) cc_final: 0.7814 (ttm) REVERT: G 228 GLU cc_start: 0.7963 (tt0) cc_final: 0.7655 (tm-30) REVERT: G 241 ASP cc_start: 0.8631 (p0) cc_final: 0.8363 (p0) REVERT: H 196 MET cc_start: 0.7848 (mmm) cc_final: 0.7560 (mmp) REVERT: H 277 MET cc_start: 0.4290 (pmm) cc_final: 0.3302 (mmt) REVERT: H 294 MET cc_start: 0.7576 (ttm) cc_final: 0.7284 (ttp) REVERT: H 315 GLN cc_start: 0.8846 (mt0) cc_final: 0.8626 (mt0) REVERT: H 317 GLN cc_start: 0.9355 (tt0) cc_final: 0.9050 (tt0) REVERT: H 346 ILE cc_start: 0.8946 (pt) cc_final: 0.8744 (pt) REVERT: H 348 MET cc_start: 0.8752 (ttm) cc_final: 0.8401 (ttm) REVERT: I 54 MET cc_start: 0.7532 (mtt) cc_final: 0.7212 (mtt) REVERT: I 103 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8357 (mttp) REVERT: I 151 GLN cc_start: 0.8453 (tt0) cc_final: 0.8172 (tt0) REVERT: J 21 PHE cc_start: 0.9108 (p90) cc_final: 0.8480 (p90) REVERT: J 118 ARG cc_start: 0.8479 (mmm160) cc_final: 0.6871 (tmm160) REVERT: K 196 GLU cc_start: 0.8134 (tp30) cc_final: 0.7523 (tp30) REVERT: K 206 ARG cc_start: 0.8785 (ttt-90) cc_final: 0.8439 (ttm-80) REVERT: K 236 GLN cc_start: 0.8546 (mt0) cc_final: 0.8269 (mt0) REVERT: K 241 ASP cc_start: 0.8855 (p0) cc_final: 0.8440 (p0) REVERT: K 249 MET cc_start: 0.8291 (ttm) cc_final: 0.7965 (ttm) REVERT: K 250 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7412 (mm-40) REVERT: L 133 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8580 (ttmt) REVERT: L 220 MET cc_start: 0.8151 (tpp) cc_final: 0.7519 (tpp) REVERT: L 277 MET cc_start: 0.3835 (pmm) cc_final: 0.2625 (mmp) REVERT: M 132 LEU cc_start: 0.9182 (mt) cc_final: 0.8964 (mp) REVERT: N 118 ARG cc_start: 0.8518 (mmm160) cc_final: 0.7250 (ttp-170) REVERT: N 128 GLU cc_start: 0.8181 (pt0) cc_final: 0.7955 (pt0) REVERT: N 157 LEU cc_start: 0.8877 (mt) cc_final: 0.8565 (mt) REVERT: O 159 VAL cc_start: 0.9367 (t) cc_final: 0.9016 (m) REVERT: O 198 ASP cc_start: 0.8295 (t0) cc_final: 0.7712 (t0) REVERT: O 241 ASP cc_start: 0.9027 (p0) cc_final: 0.8588 (p0) REVERT: P 133 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8369 (ttmt) REVERT: P 277 MET cc_start: 0.5082 (pmm) cc_final: 0.2949 (mmp) REVERT: P 305 ASP cc_start: 0.8365 (t70) cc_final: 0.8154 (t0) REVERT: P 348 MET cc_start: 0.8473 (ttm) cc_final: 0.7654 (ttm) REVERT: Q 103 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7753 (mtmm) REVERT: Q 151 GLN cc_start: 0.8566 (tt0) cc_final: 0.7846 (tt0) REVERT: R 48 LYS cc_start: 0.8898 (pttp) cc_final: 0.8497 (pttm) REVERT: R 118 ARG cc_start: 0.8683 (mmm160) cc_final: 0.7612 (tmm160) REVERT: S 125 ILE cc_start: 0.9385 (mp) cc_final: 0.9055 (mt) REVERT: S 159 VAL cc_start: 0.9446 (t) cc_final: 0.9023 (m) REVERT: S 164 MET cc_start: 0.9233 (ttm) cc_final: 0.9023 (ttm) REVERT: S 176 ASP cc_start: 0.8644 (t70) cc_final: 0.8388 (t0) REVERT: S 215 MET cc_start: 0.8146 (ttm) cc_final: 0.7849 (ttm) REVERT: S 228 GLU cc_start: 0.7964 (tt0) cc_final: 0.7680 (tm-30) REVERT: S 241 ASP cc_start: 0.8680 (p0) cc_final: 0.8393 (p0) REVERT: T 196 MET cc_start: 0.7959 (mmm) cc_final: 0.7688 (mmp) REVERT: T 277 MET cc_start: 0.4257 (pmm) cc_final: 0.3321 (mmt) REVERT: T 315 GLN cc_start: 0.8910 (mt0) cc_final: 0.8544 (mt0) REVERT: T 317 GLN cc_start: 0.9379 (tt0) cc_final: 0.9127 (tt0) REVERT: T 348 MET cc_start: 0.8756 (ttm) cc_final: 0.8397 (ttm) REVERT: U 54 MET cc_start: 0.7569 (mtt) cc_final: 0.7251 (mtt) REVERT: U 103 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8577 (mttp) REVERT: U 151 GLN cc_start: 0.8459 (tt0) cc_final: 0.8198 (tt0) REVERT: V 21 PHE cc_start: 0.9149 (p90) cc_final: 0.8571 (p90) REVERT: V 54 MET cc_start: 0.8850 (mmm) cc_final: 0.8631 (mmt) REVERT: V 118 ARG cc_start: 0.8388 (mmm160) cc_final: 0.6841 (tmm160) REVERT: W 196 GLU cc_start: 0.8160 (tp30) cc_final: 0.7555 (tp30) REVERT: W 206 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8418 (ttm-80) REVERT: W 236 GLN cc_start: 0.8597 (mt0) cc_final: 0.8192 (mt0) REVERT: W 241 ASP cc_start: 0.8833 (p0) cc_final: 0.8410 (p0) REVERT: X 133 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8583 (ttmt) REVERT: X 220 MET cc_start: 0.8191 (tpp) cc_final: 0.7628 (tpp) REVERT: X 277 MET cc_start: 0.3741 (pmm) cc_final: 0.2541 (mmp) outliers start: 0 outliers final: 0 residues processed: 975 average time/residue: 0.2363 time to fit residues: 361.8256 Evaluate side-chains 721 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 250 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN F 35 GLN F 89 GLN G 200 GLN G 204 HIS G 236 GLN H 227 GLN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN J 89 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN M 147 ASN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN O 200 GLN O 250 GLN ** P 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Q 147 ASN R 35 GLN R 89 GLN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 200 GLN S 204 HIS S 236 GLN T 227 GLN ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 147 ASN V 89 GLN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 200 GLN ** X 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.087530 restraints weight = 62140.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.090095 restraints weight = 30846.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091794 restraints weight = 18520.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092935 restraints weight = 12491.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093733 restraints weight = 9157.307| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35370 Z= 0.191 Angle : 0.636 9.605 47952 Z= 0.335 Chirality : 0.046 0.244 5244 Planarity : 0.004 0.044 6264 Dihedral : 4.762 18.345 4668 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.97 % Allowed : 12.86 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4230 helix: 1.27 (0.17), residues: 822 sheet: -0.38 (0.14), residues: 1422 loop : -1.73 (0.12), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 56 TYR 0.010 0.001 TYR B 107 PHE 0.017 0.002 PHE M 21 TRP 0.019 0.001 TRP H 209 HIS 0.005 0.001 HIS K 211 Details of bonding type rmsd covalent geometry : bond 0.00446 (35358) covalent geometry : angle 0.63611 (47952) hydrogen bonds : bond 0.04479 ( 1158) hydrogen bonds : angle 6.25136 ( 3438) Misc. bond : bond 0.00044 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 775 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8425 (ttpp) REVERT: A 47 GLU cc_start: 0.7996 (tt0) cc_final: 0.7513 (tt0) REVERT: A 54 MET cc_start: 0.8194 (mtt) cc_final: 0.7856 (mtt) REVERT: A 89 GLN cc_start: 0.8970 (tt0) cc_final: 0.8562 (tt0) REVERT: A 121 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8608 (mmtm) REVERT: B 20 LEU cc_start: 0.8989 (mt) cc_final: 0.8606 (mt) REVERT: B 98 GLU cc_start: 0.8574 (tt0) cc_final: 0.8333 (mm-30) REVERT: B 118 ARG cc_start: 0.8460 (mmm160) cc_final: 0.7195 (ttp-170) REVERT: B 157 LEU cc_start: 0.9304 (mt) cc_final: 0.9045 (mt) REVERT: C 5 GLU cc_start: 0.8561 (tp30) cc_final: 0.8133 (tp30) REVERT: C 159 VAL cc_start: 0.9268 (t) cc_final: 0.8978 (m) REVERT: C 236 GLN cc_start: 0.8692 (mt0) cc_final: 0.8486 (mt0) REVERT: D 277 MET cc_start: 0.4716 (pmm) cc_final: 0.2698 (mmp) REVERT: D 292 VAL cc_start: 0.9008 (p) cc_final: 0.8717 (m) REVERT: D 294 MET cc_start: 0.7666 (ttm) cc_final: 0.7053 (ttt) REVERT: D 348 MET cc_start: 0.8645 (ttm) cc_final: 0.8302 (ttp) REVERT: E 30 GLN cc_start: 0.8125 (tp40) cc_final: 0.7902 (tp40) REVERT: E 54 MET cc_start: 0.8184 (mtt) cc_final: 0.7864 (mtt) REVERT: E 103 LYS cc_start: 0.8414 (mmtp) cc_final: 0.7939 (mttm) REVERT: F 76 ASP cc_start: 0.8453 (t70) cc_final: 0.8099 (p0) REVERT: F 118 ARG cc_start: 0.8778 (mmm160) cc_final: 0.7470 (tmm160) REVERT: F 143 ASP cc_start: 0.8005 (t0) cc_final: 0.7646 (t0) REVERT: G 125 ILE cc_start: 0.9566 (mp) cc_final: 0.9237 (mt) REVERT: G 138 GLU cc_start: 0.8502 (tp30) cc_final: 0.8296 (tp30) REVERT: G 159 VAL cc_start: 0.9323 (t) cc_final: 0.8802 (m) REVERT: G 236 GLN cc_start: 0.9026 (mt0) cc_final: 0.8741 (mt0) REVERT: G 241 ASP cc_start: 0.8797 (p0) cc_final: 0.8441 (p0) REVERT: H 277 MET cc_start: 0.4252 (pmm) cc_final: 0.3509 (mmt) REVERT: H 294 MET cc_start: 0.7337 (ttm) cc_final: 0.6803 (ttm) REVERT: H 315 GLN cc_start: 0.8876 (mt0) cc_final: 0.8616 (mt0) REVERT: H 317 GLN cc_start: 0.9372 (tt0) cc_final: 0.9150 (tt0) REVERT: H 346 ILE cc_start: 0.8436 (pt) cc_final: 0.8085 (mt) REVERT: I 54 MET cc_start: 0.8272 (mtt) cc_final: 0.8016 (mtt) REVERT: I 103 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8194 (mttm) REVERT: I 151 GLN cc_start: 0.8392 (tt0) cc_final: 0.7619 (tt0) REVERT: J 28 LEU cc_start: 0.9254 (mm) cc_final: 0.8886 (mt) REVERT: J 76 ASP cc_start: 0.8362 (t70) cc_final: 0.7971 (p0) REVERT: J 115 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7796 (tm-30) REVERT: J 118 ARG cc_start: 0.8463 (mmm160) cc_final: 0.7076 (ttp-170) REVERT: K 13 ASN cc_start: 0.9005 (m-40) cc_final: 0.8717 (m-40) REVERT: K 134 ARG cc_start: 0.8687 (ttp-110) cc_final: 0.8337 (mtp-110) REVERT: K 143 TYR cc_start: 0.8165 (m-80) cc_final: 0.7924 (m-80) REVERT: K 154 GLU cc_start: 0.8030 (pt0) cc_final: 0.7763 (pt0) REVERT: K 199 ILE cc_start: 0.8379 (pt) cc_final: 0.8001 (pt) REVERT: K 225 SER cc_start: 0.9244 (t) cc_final: 0.8855 (p) REVERT: K 236 GLN cc_start: 0.8554 (mt0) cc_final: 0.8230 (mt0) REVERT: K 246 TYR cc_start: 0.9086 (p90) cc_final: 0.8882 (p90) REVERT: L 133 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8506 (ttmt) REVERT: L 220 MET cc_start: 0.8251 (tpp) cc_final: 0.7723 (tpp) REVERT: L 277 MET cc_start: 0.3971 (pmm) cc_final: 0.2728 (mmp) REVERT: L 346 ILE cc_start: 0.9148 (pt) cc_final: 0.8827 (mt) REVERT: M 47 GLU cc_start: 0.7976 (tt0) cc_final: 0.7491 (tt0) REVERT: M 54 MET cc_start: 0.8153 (mtt) cc_final: 0.7902 (mtt) REVERT: M 89 GLN cc_start: 0.8954 (tt0) cc_final: 0.8547 (tt0) REVERT: M 132 LEU cc_start: 0.9204 (mt) cc_final: 0.8984 (mp) REVERT: N 76 ASP cc_start: 0.8349 (t70) cc_final: 0.8139 (p0) REVERT: N 118 ARG cc_start: 0.8542 (mmm160) cc_final: 0.7180 (ttp-170) REVERT: N 157 LEU cc_start: 0.9291 (mt) cc_final: 0.9034 (mt) REVERT: O 5 GLU cc_start: 0.8573 (tp30) cc_final: 0.8156 (tp30) REVERT: O 159 VAL cc_start: 0.9260 (t) cc_final: 0.8956 (m) REVERT: O 236 GLN cc_start: 0.8685 (mt0) cc_final: 0.8462 (mt0) REVERT: P 277 MET cc_start: 0.4722 (pmm) cc_final: 0.2702 (mmp) REVERT: P 292 VAL cc_start: 0.8978 (p) cc_final: 0.8671 (m) REVERT: P 294 MET cc_start: 0.7674 (ttm) cc_final: 0.7065 (ttt) REVERT: P 348 MET cc_start: 0.8590 (ttm) cc_final: 0.8308 (ttp) REVERT: Q 30 GLN cc_start: 0.8113 (tp40) cc_final: 0.7871 (tp40) REVERT: Q 54 MET cc_start: 0.8222 (mtt) cc_final: 0.7929 (mtt) REVERT: Q 103 LYS cc_start: 0.8420 (mmtp) cc_final: 0.7936 (mttm) REVERT: Q 148 ASN cc_start: 0.8751 (m-40) cc_final: 0.8455 (m110) REVERT: R 30 GLN cc_start: 0.8343 (pm20) cc_final: 0.8048 (mm-40) REVERT: R 76 ASP cc_start: 0.8586 (t70) cc_final: 0.7995 (p0) REVERT: R 118 ARG cc_start: 0.8829 (mmm160) cc_final: 0.7481 (tmm160) REVERT: S 125 ILE cc_start: 0.9580 (mp) cc_final: 0.9236 (mt) REVERT: S 164 MET cc_start: 0.9121 (ttm) cc_final: 0.8909 (ttm) REVERT: S 241 ASP cc_start: 0.8797 (p0) cc_final: 0.8432 (p0) REVERT: T 277 MET cc_start: 0.3946 (pmm) cc_final: 0.3233 (mmt) REVERT: T 315 GLN cc_start: 0.8771 (mt0) cc_final: 0.8454 (mt0) REVERT: T 317 GLN cc_start: 0.9392 (tt0) cc_final: 0.9086 (tt0) REVERT: T 346 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8416 (mt) REVERT: U 21 PHE cc_start: 0.8933 (p90) cc_final: 0.8691 (p90) REVERT: U 22 GLN cc_start: 0.8802 (mt0) cc_final: 0.8532 (mt0) REVERT: U 30 GLN cc_start: 0.7730 (tp40) cc_final: 0.6666 (tp40) REVERT: U 54 MET cc_start: 0.8260 (mtt) cc_final: 0.7997 (mtt) REVERT: U 103 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8346 (mttm) REVERT: U 139 GLU cc_start: 0.8050 (tp30) cc_final: 0.7734 (tp30) REVERT: U 142 LEU cc_start: 0.8422 (tt) cc_final: 0.8169 (tp) REVERT: U 151 GLN cc_start: 0.8421 (tt0) cc_final: 0.7592 (tt0) REVERT: V 21 PHE cc_start: 0.9175 (p90) cc_final: 0.8592 (p90) REVERT: V 54 MET cc_start: 0.8534 (mmm) cc_final: 0.8302 (mmt) REVERT: V 76 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7962 (p0) REVERT: V 115 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7789 (tm-30) REVERT: V 118 ARG cc_start: 0.8552 (mmm160) cc_final: 0.7153 (tmm160) REVERT: W 13 ASN cc_start: 0.9001 (m-40) cc_final: 0.8728 (m-40) REVERT: W 134 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8332 (mtp-110) REVERT: W 143 TYR cc_start: 0.8146 (m-80) cc_final: 0.7921 (m-80) REVERT: W 185 VAL cc_start: 0.8851 (t) cc_final: 0.8609 (p) REVERT: W 199 ILE cc_start: 0.8333 (pt) cc_final: 0.7974 (pt) REVERT: W 225 SER cc_start: 0.9224 (t) cc_final: 0.8780 (p) REVERT: W 229 LEU cc_start: 0.9231 (pp) cc_final: 0.8929 (pp) REVERT: W 236 GLN cc_start: 0.8549 (mt0) cc_final: 0.8211 (mt0) REVERT: X 133 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8481 (ttmt) REVERT: X 220 MET cc_start: 0.8183 (tpp) cc_final: 0.7620 (tpp) REVERT: X 277 MET cc_start: 0.3899 (pmm) cc_final: 0.2704 (mmp) outliers start: 74 outliers final: 47 residues processed: 819 average time/residue: 0.2328 time to fit residues: 299.8373 Evaluate side-chains 719 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 670 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 74 MET Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 223 SER Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 346 ILE Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 103 LYS Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain W residue 176 ASP Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 275 optimal weight: 0.5980 chunk 305 optimal weight: 0.8980 chunk 347 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 419 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 351 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 236 GLN T 141 HIS ** T 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.088705 restraints weight = 61863.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.091252 restraints weight = 30242.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092963 restraints weight = 17998.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.094076 restraints weight = 12078.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094845 restraints weight = 8852.387| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35370 Z= 0.139 Angle : 0.569 9.025 47952 Z= 0.298 Chirality : 0.043 0.177 5244 Planarity : 0.004 0.057 6264 Dihedral : 4.576 18.714 4668 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.66 % Allowed : 16.53 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.12), residues: 4230 helix: 1.19 (0.17), residues: 858 sheet: -0.50 (0.14), residues: 1452 loop : -1.78 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 81 TYR 0.009 0.001 TYR J 27 PHE 0.017 0.001 PHE H 304 TRP 0.013 0.001 TRP P 209 HIS 0.003 0.001 HIS S 211 Details of bonding type rmsd covalent geometry : bond 0.00323 (35358) covalent geometry : angle 0.56897 (47952) hydrogen bonds : bond 0.03895 ( 1158) hydrogen bonds : angle 5.73812 ( 3438) Misc. bond : bond 0.00042 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 746 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8510 (ttpp) REVERT: A 47 GLU cc_start: 0.7989 (tt0) cc_final: 0.7446 (tt0) REVERT: A 54 MET cc_start: 0.8016 (mtt) cc_final: 0.7496 (mtt) REVERT: A 89 GLN cc_start: 0.8920 (tt0) cc_final: 0.8580 (tt0) REVERT: A 148 ASN cc_start: 0.8273 (m-40) cc_final: 0.7987 (m-40) REVERT: B 20 LEU cc_start: 0.8875 (mt) cc_final: 0.8213 (mt) REVERT: B 54 MET cc_start: 0.8924 (mmm) cc_final: 0.8598 (mmm) REVERT: B 118 ARG cc_start: 0.8488 (mmm160) cc_final: 0.7120 (ttp-170) REVERT: B 157 LEU cc_start: 0.9321 (mt) cc_final: 0.8950 (mt) REVERT: C 5 GLU cc_start: 0.8584 (tp30) cc_final: 0.8118 (tp30) REVERT: C 159 VAL cc_start: 0.9281 (t) cc_final: 0.8977 (m) REVERT: D 137 ASP cc_start: 0.8794 (m-30) cc_final: 0.8577 (m-30) REVERT: D 210 ASP cc_start: 0.7812 (t0) cc_final: 0.7449 (m-30) REVERT: D 277 MET cc_start: 0.3728 (pmm) cc_final: 0.3321 (mmp) REVERT: D 292 VAL cc_start: 0.8936 (p) cc_final: 0.8675 (m) REVERT: D 294 MET cc_start: 0.7613 (ttm) cc_final: 0.7057 (ttp) REVERT: D 348 MET cc_start: 0.8700 (ttm) cc_final: 0.8370 (ttt) REVERT: E 30 GLN cc_start: 0.8153 (tp40) cc_final: 0.7923 (tp40) REVERT: E 54 MET cc_start: 0.7927 (mtt) cc_final: 0.7119 (mtt) REVERT: E 103 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8254 (mttm) REVERT: E 148 ASN cc_start: 0.8806 (m-40) cc_final: 0.8590 (m-40) REVERT: E 151 GLN cc_start: 0.8874 (tt0) cc_final: 0.8476 (mt0) REVERT: F 118 ARG cc_start: 0.8799 (mmm160) cc_final: 0.7499 (tmm160) REVERT: G 125 ILE cc_start: 0.9595 (mp) cc_final: 0.9174 (mt) REVERT: G 159 VAL cc_start: 0.9355 (t) cc_final: 0.8801 (m) REVERT: G 236 GLN cc_start: 0.9058 (mt0) cc_final: 0.8731 (mt0) REVERT: G 241 ASP cc_start: 0.8800 (p0) cc_final: 0.8446 (p0) REVERT: H 210 ASP cc_start: 0.8549 (t0) cc_final: 0.8316 (t0) REVERT: H 211 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7700 (mp) REVERT: H 294 MET cc_start: 0.7348 (ttm) cc_final: 0.6746 (ttm) REVERT: H 315 GLN cc_start: 0.8609 (mt0) cc_final: 0.8306 (mt0) REVERT: H 317 GLN cc_start: 0.9343 (tt0) cc_final: 0.8837 (tm-30) REVERT: I 54 MET cc_start: 0.7756 (mtt) cc_final: 0.7270 (mtt) REVERT: I 103 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8256 (mttm) REVERT: I 151 GLN cc_start: 0.8493 (tt0) cc_final: 0.8028 (tt0) REVERT: J 21 PHE cc_start: 0.9065 (p90) cc_final: 0.8532 (p90) REVERT: J 76 ASP cc_start: 0.8335 (t70) cc_final: 0.7904 (p0) REVERT: J 115 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7748 (tm-30) REVERT: J 118 ARG cc_start: 0.8536 (mmm160) cc_final: 0.6969 (ttp-170) REVERT: K 13 ASN cc_start: 0.8991 (m-40) cc_final: 0.8718 (m-40) REVERT: K 134 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8270 (mtm110) REVERT: K 143 TYR cc_start: 0.8037 (m-80) cc_final: 0.7731 (m-80) REVERT: K 198 ASP cc_start: 0.8360 (t0) cc_final: 0.8145 (t0) REVERT: K 199 ILE cc_start: 0.8319 (pt) cc_final: 0.8016 (pt) REVERT: K 225 SER cc_start: 0.9266 (t) cc_final: 0.8832 (p) REVERT: K 236 GLN cc_start: 0.8625 (mt0) cc_final: 0.8316 (mt0) REVERT: L 220 MET cc_start: 0.8153 (tpp) cc_final: 0.7632 (tpp) REVERT: L 277 MET cc_start: 0.3280 (pmm) cc_final: 0.2430 (mmp) REVERT: L 317 GLN cc_start: 0.9513 (tt0) cc_final: 0.9159 (tm-30) REVERT: L 346 ILE cc_start: 0.9116 (pt) cc_final: 0.8837 (mt) REVERT: M 47 GLU cc_start: 0.7962 (tt0) cc_final: 0.7438 (tt0) REVERT: M 54 MET cc_start: 0.7932 (mtt) cc_final: 0.7467 (mtt) REVERT: M 89 GLN cc_start: 0.8907 (tt0) cc_final: 0.8520 (tt0) REVERT: N 54 MET cc_start: 0.9032 (mmt) cc_final: 0.8722 (mmt) REVERT: N 118 ARG cc_start: 0.8562 (mmm160) cc_final: 0.7123 (ttp-170) REVERT: N 157 LEU cc_start: 0.9299 (mt) cc_final: 0.8999 (mt) REVERT: O 5 GLU cc_start: 0.8585 (tp30) cc_final: 0.8217 (tp30) REVERT: O 159 VAL cc_start: 0.9234 (t) cc_final: 0.8947 (m) REVERT: P 137 ASP cc_start: 0.8769 (m-30) cc_final: 0.8556 (m-30) REVERT: P 210 ASP cc_start: 0.7892 (t0) cc_final: 0.7496 (m-30) REVERT: P 277 MET cc_start: 0.4201 (pmm) cc_final: 0.3327 (mmp) REVERT: P 292 VAL cc_start: 0.8909 (p) cc_final: 0.8630 (m) REVERT: P 294 MET cc_start: 0.7618 (ttm) cc_final: 0.7050 (ttp) REVERT: P 305 ASP cc_start: 0.8561 (t70) cc_final: 0.8311 (t0) REVERT: P 348 MET cc_start: 0.8592 (ttm) cc_final: 0.8124 (ttm) REVERT: Q 30 GLN cc_start: 0.8146 (tp40) cc_final: 0.7884 (tp40) REVERT: Q 54 MET cc_start: 0.7951 (mtt) cc_final: 0.7211 (mtt) REVERT: Q 103 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8233 (mttm) REVERT: Q 151 GLN cc_start: 0.8874 (tt0) cc_final: 0.8423 (mt0) REVERT: R 75 ASN cc_start: 0.9261 (t0) cc_final: 0.8944 (t0) REVERT: R 76 ASP cc_start: 0.8409 (t70) cc_final: 0.8116 (t70) REVERT: R 118 ARG cc_start: 0.8773 (mmm160) cc_final: 0.7471 (tmm160) REVERT: R 143 ASP cc_start: 0.8009 (t0) cc_final: 0.7586 (t0) REVERT: S 125 ILE cc_start: 0.9580 (mp) cc_final: 0.9159 (mt) REVERT: S 159 VAL cc_start: 0.9292 (t) cc_final: 0.8803 (m) REVERT: S 236 GLN cc_start: 0.9018 (mt0) cc_final: 0.8799 (mt0) REVERT: S 241 ASP cc_start: 0.8836 (p0) cc_final: 0.8446 (p0) REVERT: T 277 MET cc_start: 0.3209 (pmm) cc_final: 0.2928 (mmt) REVERT: T 317 GLN cc_start: 0.9367 (tt0) cc_final: 0.8822 (tm-30) REVERT: U 22 GLN cc_start: 0.8751 (mt0) cc_final: 0.8503 (mt0) REVERT: U 30 GLN cc_start: 0.7840 (tp40) cc_final: 0.6676 (tp40) REVERT: U 54 MET cc_start: 0.7733 (mtt) cc_final: 0.7244 (mtt) REVERT: U 103 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8207 (mttp) REVERT: U 151 GLN cc_start: 0.8512 (tt0) cc_final: 0.8145 (tt0) REVERT: V 21 PHE cc_start: 0.9112 (p90) cc_final: 0.8576 (p90) REVERT: V 115 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7841 (tm-30) REVERT: V 118 ARG cc_start: 0.8515 (mmm160) cc_final: 0.7145 (tmm160) REVERT: W 13 ASN cc_start: 0.8985 (m-40) cc_final: 0.8726 (m-40) REVERT: W 134 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8303 (mtp-110) REVERT: W 143 TYR cc_start: 0.8018 (m-80) cc_final: 0.7710 (m-80) REVERT: W 185 VAL cc_start: 0.8896 (t) cc_final: 0.8677 (p) REVERT: W 199 ILE cc_start: 0.8276 (pt) cc_final: 0.7930 (pt) REVERT: W 225 SER cc_start: 0.9261 (t) cc_final: 0.8840 (p) REVERT: W 229 LEU cc_start: 0.9173 (pp) cc_final: 0.8964 (pp) REVERT: W 236 GLN cc_start: 0.8553 (mt0) cc_final: 0.8232 (mt0) REVERT: W 250 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7549 (mm-40) REVERT: X 53 GLN cc_start: 0.7184 (mp10) cc_final: 0.6846 (mt0) REVERT: X 80 MET cc_start: 0.8271 (ttp) cc_final: 0.7850 (ttm) REVERT: X 133 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8231 (ttmt) REVERT: X 210 ASP cc_start: 0.7880 (t0) cc_final: 0.7640 (m-30) REVERT: X 220 MET cc_start: 0.8089 (tpp) cc_final: 0.7531 (tpp) REVERT: X 277 MET cc_start: 0.3226 (pmm) cc_final: 0.2410 (mmp) REVERT: X 317 GLN cc_start: 0.9510 (tt0) cc_final: 0.9164 (tm-30) outliers start: 100 outliers final: 72 residues processed: 817 average time/residue: 0.2197 time to fit residues: 286.5475 Evaluate side-chains 756 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 683 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 83 GLN Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 346 ILE Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 74 MET Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain W residue 176 ASP Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 65 optimal weight: 0.0870 chunk 199 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 413 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 HIS ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN L 53 GLN ** L 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 200 GLN V 59 ASN W 193 GLN W 200 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.091632 restraints weight = 60889.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094227 restraints weight = 29987.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095946 restraints weight = 17781.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097096 restraints weight = 11829.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097918 restraints weight = 8592.383| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35370 Z= 0.109 Angle : 0.540 9.243 47952 Z= 0.281 Chirality : 0.042 0.179 5244 Planarity : 0.003 0.044 6264 Dihedral : 4.362 16.549 4668 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.04 % Allowed : 18.24 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4230 helix: 1.31 (0.18), residues: 858 sheet: -0.42 (0.14), residues: 1452 loop : -1.78 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 134 TYR 0.010 0.001 TYR R 27 PHE 0.020 0.001 PHE B 53 TRP 0.008 0.001 TRP H 209 HIS 0.003 0.000 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00247 (35358) covalent geometry : angle 0.54013 (47952) hydrogen bonds : bond 0.03433 ( 1158) hydrogen bonds : angle 5.40600 ( 3438) Misc. bond : bond 0.00032 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 800 time to evaluate : 1.200 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: A 37 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8477 (ttpp) REVERT: A 47 GLU cc_start: 0.7917 (tt0) cc_final: 0.7367 (tt0) REVERT: A 54 MET cc_start: 0.8010 (mtt) cc_final: 0.7583 (mtt) REVERT: A 89 GLN cc_start: 0.8906 (tt0) cc_final: 0.8537 (tt0) REVERT: B 98 GLU cc_start: 0.8560 (tt0) cc_final: 0.8297 (mm-30) REVERT: B 118 ARG cc_start: 0.8462 (mmm160) cc_final: 0.7097 (ttp-170) REVERT: B 157 LEU cc_start: 0.9315 (mt) cc_final: 0.9019 (mt) REVERT: C 5 GLU cc_start: 0.8485 (tp30) cc_final: 0.8124 (tp30) REVERT: C 137 TYR cc_start: 0.8961 (p90) cc_final: 0.8731 (p90) REVERT: C 159 VAL cc_start: 0.9233 (t) cc_final: 0.8986 (m) REVERT: C 241 ASP cc_start: 0.8796 (p0) cc_final: 0.8368 (p0) REVERT: D 210 ASP cc_start: 0.7936 (t0) cc_final: 0.7619 (m-30) REVERT: D 277 MET cc_start: 0.3841 (OUTLIER) cc_final: 0.3259 (mmp) REVERT: D 292 VAL cc_start: 0.8898 (p) cc_final: 0.8627 (m) REVERT: D 294 MET cc_start: 0.7478 (ttm) cc_final: 0.7032 (ttp) REVERT: E 103 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8265 (mttm) REVERT: E 148 ASN cc_start: 0.8813 (m-40) cc_final: 0.8585 (m-40) REVERT: E 151 GLN cc_start: 0.8832 (tt0) cc_final: 0.8480 (mt0) REVERT: F 48 LYS cc_start: 0.9335 (pttt) cc_final: 0.8326 (pttt) REVERT: F 59 ASN cc_start: 0.9093 (m-40) cc_final: 0.8232 (m-40) REVERT: F 118 ARG cc_start: 0.8739 (mmm160) cc_final: 0.7530 (tmm160) REVERT: F 143 ASP cc_start: 0.7917 (t0) cc_final: 0.7519 (t0) REVERT: G 125 ILE cc_start: 0.9599 (mp) cc_final: 0.9157 (mt) REVERT: G 129 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8713 (tmmt) REVERT: G 156 ASP cc_start: 0.8559 (m-30) cc_final: 0.8227 (m-30) REVERT: G 159 VAL cc_start: 0.9345 (t) cc_final: 0.8795 (m) REVERT: G 236 GLN cc_start: 0.9035 (mt0) cc_final: 0.8733 (mt0) REVERT: G 241 ASP cc_start: 0.8803 (p0) cc_final: 0.8476 (p0) REVERT: G 250 GLN cc_start: 0.7739 (tp40) cc_final: 0.7534 (tp40) REVERT: H 294 MET cc_start: 0.7285 (ttm) cc_final: 0.6711 (ttm) REVERT: H 317 GLN cc_start: 0.9325 (tt0) cc_final: 0.8859 (tm-30) REVERT: I 54 MET cc_start: 0.7439 (mtt) cc_final: 0.6878 (mtt) REVERT: I 151 GLN cc_start: 0.8529 (tt0) cc_final: 0.7930 (tt0) REVERT: J 21 PHE cc_start: 0.9016 (p90) cc_final: 0.8476 (p90) REVERT: J 115 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7860 (tm-30) REVERT: J 118 ARG cc_start: 0.8443 (mmm160) cc_final: 0.7076 (tmm160) REVERT: K 13 ASN cc_start: 0.8938 (m-40) cc_final: 0.8611 (m-40) REVERT: K 143 TYR cc_start: 0.7990 (m-80) cc_final: 0.7762 (m-80) REVERT: K 199 ILE cc_start: 0.8157 (pt) cc_final: 0.7816 (pt) REVERT: K 225 SER cc_start: 0.9239 (t) cc_final: 0.8866 (p) REVERT: K 236 GLN cc_start: 0.8600 (mt0) cc_final: 0.8247 (mt0) REVERT: L 80 MET cc_start: 0.8115 (ttp) cc_final: 0.7787 (ttm) REVERT: L 220 MET cc_start: 0.8072 (tpp) cc_final: 0.7466 (tpp) REVERT: L 277 MET cc_start: 0.3206 (OUTLIER) cc_final: 0.2947 (mmp) REVERT: L 294 MET cc_start: 0.7244 (ttp) cc_final: 0.6976 (ttm) REVERT: L 317 GLN cc_start: 0.9316 (tt0) cc_final: 0.9052 (tm-30) REVERT: L 346 ILE cc_start: 0.9131 (pt) cc_final: 0.8882 (mt) REVERT: L 348 MET cc_start: 0.8596 (ttm) cc_final: 0.8271 (ttm) REVERT: M 47 GLU cc_start: 0.7893 (tt0) cc_final: 0.7386 (tt0) REVERT: M 54 MET cc_start: 0.8044 (mtt) cc_final: 0.7656 (mtt) REVERT: M 89 GLN cc_start: 0.8894 (tt0) cc_final: 0.8517 (tt0) REVERT: M 148 ASN cc_start: 0.8382 (m-40) cc_final: 0.8127 (m-40) REVERT: N 28 LEU cc_start: 0.9432 (mm) cc_final: 0.9226 (mp) REVERT: N 98 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6937 (mm-30) REVERT: N 118 ARG cc_start: 0.8450 (mmm160) cc_final: 0.7137 (ttp-170) REVERT: N 157 LEU cc_start: 0.9345 (mt) cc_final: 0.9040 (mt) REVERT: O 5 GLU cc_start: 0.8510 (tp30) cc_final: 0.8138 (tp30) REVERT: O 137 TYR cc_start: 0.8950 (p90) cc_final: 0.8743 (p90) REVERT: O 159 VAL cc_start: 0.9247 (t) cc_final: 0.9002 (m) REVERT: O 198 ASP cc_start: 0.7993 (t0) cc_final: 0.7762 (t0) REVERT: O 241 ASP cc_start: 0.8802 (p0) cc_final: 0.8399 (p0) REVERT: P 210 ASP cc_start: 0.7792 (t0) cc_final: 0.7474 (m-30) REVERT: P 277 MET cc_start: 0.3647 (OUTLIER) cc_final: 0.3279 (mmp) REVERT: P 292 VAL cc_start: 0.8867 (p) cc_final: 0.8573 (m) REVERT: P 294 MET cc_start: 0.7500 (ttm) cc_final: 0.7048 (ttp) REVERT: P 305 ASP cc_start: 0.8586 (t70) cc_final: 0.8360 (t0) REVERT: Q 103 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8249 (mttm) REVERT: Q 148 ASN cc_start: 0.8794 (m-40) cc_final: 0.8563 (m-40) REVERT: Q 151 GLN cc_start: 0.8818 (tt0) cc_final: 0.8433 (mt0) REVERT: R 37 LYS cc_start: 0.8586 (tttm) cc_final: 0.8274 (tmtt) REVERT: R 48 LYS cc_start: 0.9350 (pttt) cc_final: 0.8343 (pttt) REVERT: R 59 ASN cc_start: 0.9124 (m-40) cc_final: 0.8257 (m-40) REVERT: R 67 ASP cc_start: 0.8149 (p0) cc_final: 0.7902 (p0) REVERT: R 118 ARG cc_start: 0.8748 (mmm160) cc_final: 0.7497 (tmm160) REVERT: R 141 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8118 (mm-40) REVERT: S 125 ILE cc_start: 0.9582 (mp) cc_final: 0.9117 (mt) REVERT: S 156 ASP cc_start: 0.8570 (m-30) cc_final: 0.8174 (m-30) REVERT: S 159 VAL cc_start: 0.9342 (t) cc_final: 0.8814 (m) REVERT: S 228 GLU cc_start: 0.8058 (tt0) cc_final: 0.7815 (tm-30) REVERT: S 236 GLN cc_start: 0.8949 (mt0) cc_final: 0.8735 (mt0) REVERT: S 241 ASP cc_start: 0.8813 (p0) cc_final: 0.8454 (p0) REVERT: T 210 ASP cc_start: 0.7925 (t0) cc_final: 0.7571 (m-30) REVERT: T 317 GLN cc_start: 0.9303 (tt0) cc_final: 0.8737 (tm-30) REVERT: U 14 ASP cc_start: 0.7547 (m-30) cc_final: 0.7318 (m-30) REVERT: U 30 GLN cc_start: 0.7863 (tp40) cc_final: 0.6765 (tp40) REVERT: U 54 MET cc_start: 0.7397 (mtt) cc_final: 0.6875 (mtt) REVERT: U 151 GLN cc_start: 0.8562 (tt0) cc_final: 0.8158 (tt0) REVERT: V 21 PHE cc_start: 0.9116 (p90) cc_final: 0.8622 (p90) REVERT: V 57 LYS cc_start: 0.9162 (mttm) cc_final: 0.8826 (mttt) REVERT: V 115 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7870 (tm-30) REVERT: V 118 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7093 (tmm160) REVERT: W 13 ASN cc_start: 0.8908 (m-40) cc_final: 0.8578 (m-40) REVERT: W 134 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8399 (mtm110) REVERT: W 185 VAL cc_start: 0.8905 (t) cc_final: 0.8655 (p) REVERT: W 199 ILE cc_start: 0.8123 (pt) cc_final: 0.7767 (pt) REVERT: W 225 SER cc_start: 0.9249 (t) cc_final: 0.8903 (p) REVERT: W 229 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8943 (pp) REVERT: W 236 GLN cc_start: 0.8522 (mt0) cc_final: 0.8192 (mt0) REVERT: W 250 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7599 (mm-40) REVERT: X 133 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8474 (ttmt) REVERT: X 220 MET cc_start: 0.8006 (tpp) cc_final: 0.7434 (tpp) REVERT: X 317 GLN cc_start: 0.9472 (tt0) cc_final: 0.9265 (tm-30) REVERT: X 348 MET cc_start: 0.8614 (ttm) cc_final: 0.8249 (ttm) outliers start: 114 outliers final: 79 residues processed: 872 average time/residue: 0.2186 time to fit residues: 307.6435 Evaluate side-chains 815 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 732 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 346 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 74 MET Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 321 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 390 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 309 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 204 HIS D 227 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN G 200 GLN J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 HIS L 227 GLN L 355 ASN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN O 204 HIS P 227 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN U 147 ASN V 59 ASN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 193 GLN W 204 HIS X 227 GLN X 355 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.084935 restraints weight = 62863.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087437 restraints weight = 31210.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.089103 restraints weight = 18700.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090213 restraints weight = 12706.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.090961 restraints weight = 9357.569| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 35370 Z= 0.259 Angle : 0.640 8.342 47952 Z= 0.335 Chirality : 0.046 0.192 5244 Planarity : 0.004 0.046 6264 Dihedral : 4.824 19.412 4668 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.34 % Allowed : 18.96 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4230 helix: 1.25 (0.17), residues: 846 sheet: -0.52 (0.14), residues: 1458 loop : -1.83 (0.12), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 134 TYR 0.029 0.002 TYR H 228 PHE 0.027 0.002 PHE I 21 TRP 0.012 0.001 TRP Q 69 HIS 0.005 0.002 HIS W 204 Details of bonding type rmsd covalent geometry : bond 0.00617 (35358) covalent geometry : angle 0.64010 (47952) hydrogen bonds : bond 0.03989 ( 1158) hydrogen bonds : angle 5.58502 ( 3438) Misc. bond : bond 0.00073 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 675 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8098 (mtt) cc_final: 0.7625 (mtt) REVERT: A 89 GLN cc_start: 0.8939 (tt0) cc_final: 0.8714 (tt0) REVERT: B 54 MET cc_start: 0.8950 (mmt) cc_final: 0.8513 (mmt) REVERT: B 84 LYS cc_start: 0.9059 (mttt) cc_final: 0.8693 (mtpt) REVERT: B 118 ARG cc_start: 0.8418 (mmm160) cc_final: 0.7222 (ttp-170) REVERT: C 5 GLU cc_start: 0.8538 (tp30) cc_final: 0.8184 (tp30) REVERT: C 137 TYR cc_start: 0.9047 (p90) cc_final: 0.8747 (p90) REVERT: C 198 ASP cc_start: 0.8202 (t0) cc_final: 0.7960 (t0) REVERT: C 204 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.6995 (p-80) REVERT: C 224 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8862 (m) REVERT: C 241 ASP cc_start: 0.8840 (p0) cc_final: 0.8491 (p0) REVERT: D 277 MET cc_start: 0.3605 (OUTLIER) cc_final: 0.3278 (mmp) REVERT: D 294 MET cc_start: 0.7811 (ttm) cc_final: 0.7099 (ttt) REVERT: D 355 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8360 (m110) REVERT: E 54 MET cc_start: 0.7810 (mtt) cc_final: 0.6778 (mtt) REVERT: E 103 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8320 (mttm) REVERT: E 139 GLU cc_start: 0.7914 (tp30) cc_final: 0.7677 (tp30) REVERT: E 151 GLN cc_start: 0.8926 (tt0) cc_final: 0.8523 (mt0) REVERT: G 125 ILE cc_start: 0.9604 (mp) cc_final: 0.9240 (mt) REVERT: G 236 GLN cc_start: 0.9042 (mt0) cc_final: 0.8701 (mt0) REVERT: H 210 ASP cc_start: 0.8583 (t0) cc_final: 0.7723 (m-30) REVERT: H 211 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8110 (mp) REVERT: H 294 MET cc_start: 0.7581 (ttm) cc_final: 0.6862 (ttm) REVERT: I 22 GLN cc_start: 0.8924 (mt0) cc_final: 0.8618 (mt0) REVERT: I 30 GLN cc_start: 0.8062 (tp40) cc_final: 0.7011 (tp40) REVERT: I 37 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8639 (ttpp) REVERT: I 54 MET cc_start: 0.7939 (mtt) cc_final: 0.7260 (mtt) REVERT: I 75 ASN cc_start: 0.8984 (t0) cc_final: 0.8622 (t0) REVERT: I 141 GLN cc_start: 0.8735 (tp40) cc_final: 0.8429 (tp40) REVERT: I 151 GLN cc_start: 0.8469 (tt0) cc_final: 0.7984 (tt0) REVERT: J 21 PHE cc_start: 0.9146 (p90) cc_final: 0.8684 (p90) REVERT: J 118 ARG cc_start: 0.8466 (mmm160) cc_final: 0.6860 (ttp-170) REVERT: K 13 ASN cc_start: 0.9039 (m-40) cc_final: 0.8723 (m-40) REVERT: K 130 MET cc_start: 0.9142 (tpp) cc_final: 0.8827 (mpp) REVERT: K 134 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8129 (mtp-110) REVERT: K 204 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7654 (p-80) REVERT: K 224 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8762 (m) REVERT: K 225 SER cc_start: 0.9306 (t) cc_final: 0.9070 (p) REVERT: K 236 GLN cc_start: 0.8634 (mt0) cc_final: 0.8240 (mt0) REVERT: L 220 MET cc_start: 0.8249 (tpp) cc_final: 0.7678 (tpp) REVERT: L 277 MET cc_start: 0.3603 (OUTLIER) cc_final: 0.3124 (mmp) REVERT: L 317 GLN cc_start: 0.9541 (tt0) cc_final: 0.9206 (tm-30) REVERT: L 348 MET cc_start: 0.8687 (ttm) cc_final: 0.8426 (ttm) REVERT: M 54 MET cc_start: 0.8033 (mtt) cc_final: 0.7510 (mtt) REVERT: M 89 GLN cc_start: 0.8915 (tt0) cc_final: 0.8691 (tt0) REVERT: M 132 LEU cc_start: 0.9089 (mt) cc_final: 0.8884 (tp) REVERT: N 24 GLU cc_start: 0.8258 (pt0) cc_final: 0.7815 (pm20) REVERT: N 30 GLN cc_start: 0.8207 (pm20) cc_final: 0.7804 (mm-40) REVERT: N 54 MET cc_start: 0.9001 (mmt) cc_final: 0.8630 (mmt) REVERT: N 118 ARG cc_start: 0.8432 (mmm160) cc_final: 0.7219 (ttp-170) REVERT: N 126 GLU cc_start: 0.8346 (tt0) cc_final: 0.8110 (tt0) REVERT: O 5 GLU cc_start: 0.8548 (tp30) cc_final: 0.8195 (tp30) REVERT: O 137 TYR cc_start: 0.9043 (p90) cc_final: 0.8762 (p90) REVERT: O 204 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.7012 (p-80) REVERT: O 224 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8886 (m) REVERT: O 229 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8846 (pp) REVERT: O 241 ASP cc_start: 0.8791 (p0) cc_final: 0.8474 (p0) REVERT: P 277 MET cc_start: 0.3921 (OUTLIER) cc_final: 0.3565 (mmp) REVERT: P 305 ASP cc_start: 0.8423 (t70) cc_final: 0.8205 (t0) REVERT: P 348 MET cc_start: 0.8587 (ttp) cc_final: 0.8339 (ttp) REVERT: P 355 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8207 (m110) REVERT: Q 54 MET cc_start: 0.7799 (mtt) cc_final: 0.6777 (mtt) REVERT: Q 103 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8302 (mttm) REVERT: Q 151 GLN cc_start: 0.8948 (tt0) cc_final: 0.8578 (mt0) REVERT: R 67 ASP cc_start: 0.8210 (p0) cc_final: 0.7983 (p0) REVERT: S 21 MET cc_start: 0.8535 (mtp) cc_final: 0.8192 (mtp) REVERT: S 125 ILE cc_start: 0.9591 (mp) cc_final: 0.9235 (mt) REVERT: S 236 GLN cc_start: 0.8962 (mt0) cc_final: 0.8736 (mt0) REVERT: S 241 ASP cc_start: 0.8884 (p0) cc_final: 0.8649 (p0) REVERT: T 210 ASP cc_start: 0.8655 (t0) cc_final: 0.8183 (m-30) REVERT: T 211 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8167 (mp) REVERT: U 30 GLN cc_start: 0.7898 (tp40) cc_final: 0.6949 (tp40) REVERT: U 54 MET cc_start: 0.7888 (mtt) cc_final: 0.7187 (mtt) REVERT: U 75 ASN cc_start: 0.8983 (t0) cc_final: 0.8591 (t0) REVERT: V 21 PHE cc_start: 0.9150 (p90) cc_final: 0.8736 (p90) REVERT: V 115 GLN cc_start: 0.8827 (tm-30) cc_final: 0.7862 (tm-30) REVERT: V 118 ARG cc_start: 0.8527 (mmm160) cc_final: 0.6873 (ttp-170) REVERT: V 139 GLU cc_start: 0.7093 (mp0) cc_final: 0.6879 (pm20) REVERT: W 13 ASN cc_start: 0.9051 (m-40) cc_final: 0.8760 (m-40) REVERT: W 130 MET cc_start: 0.9172 (tpp) cc_final: 0.8776 (mpp) REVERT: W 134 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8384 (mtp-110) REVERT: W 204 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7737 (p-80) REVERT: W 224 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8843 (m) REVERT: W 225 SER cc_start: 0.9290 (t) cc_final: 0.9087 (p) REVERT: W 229 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8937 (pp) REVERT: W 236 GLN cc_start: 0.8568 (mt0) cc_final: 0.8168 (mt0) REVERT: X 53 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6866 (mt0) REVERT: X 80 MET cc_start: 0.8228 (ttp) cc_final: 0.7910 (ttm) REVERT: X 133 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8441 (ttmt) REVERT: X 210 ASP cc_start: 0.8139 (t0) cc_final: 0.7904 (m-30) REVERT: X 220 MET cc_start: 0.8185 (tpp) cc_final: 0.7632 (tpp) REVERT: X 294 MET cc_start: 0.7387 (ttt) cc_final: 0.7150 (ttm) outliers start: 163 outliers final: 119 residues processed: 792 average time/residue: 0.2156 time to fit residues: 274.4876 Evaluate side-chains 760 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 624 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 224 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 220 MET Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain P residue 355 ASN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 121 LYS Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 237 ILE Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 346 ILE Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 176 ASP Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 295 VAL Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 350 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 278 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 204 HIS D 141 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN O 204 HIS ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN U 147 ASN ** U 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.088069 restraints weight = 61529.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090645 restraints weight = 30431.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092314 restraints weight = 18141.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093483 restraints weight = 12251.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094272 restraints weight = 8912.910| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35370 Z= 0.124 Angle : 0.566 7.606 47952 Z= 0.294 Chirality : 0.043 0.180 5244 Planarity : 0.003 0.037 6264 Dihedral : 4.540 19.281 4668 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.97 % Allowed : 20.61 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4230 helix: 1.40 (0.18), residues: 846 sheet: -0.50 (0.14), residues: 1422 loop : -1.85 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 134 TYR 0.032 0.001 TYR X 228 PHE 0.021 0.001 PHE I 21 TRP 0.008 0.001 TRP A 162 HIS 0.011 0.002 HIS W 204 Details of bonding type rmsd covalent geometry : bond 0.00287 (35358) covalent geometry : angle 0.56607 (47952) hydrogen bonds : bond 0.03430 ( 1158) hydrogen bonds : angle 5.38098 ( 3438) Misc. bond : bond 0.00044 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 709 time to evaluate : 0.909 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: A 37 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8487 (ttpp) REVERT: A 54 MET cc_start: 0.8034 (mtt) cc_final: 0.7677 (mtt) REVERT: A 89 GLN cc_start: 0.8919 (tt0) cc_final: 0.8669 (tt0) REVERT: B 118 ARG cc_start: 0.8462 (mmm160) cc_final: 0.7034 (ttp-170) REVERT: C 5 GLU cc_start: 0.8502 (tp30) cc_final: 0.8144 (tp30) REVERT: C 181 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8665 (m) REVERT: C 204 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.6617 (p-80) REVERT: C 224 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8863 (m) REVERT: C 241 ASP cc_start: 0.8763 (p0) cc_final: 0.8432 (p0) REVERT: D 210 ASP cc_start: 0.8025 (t0) cc_final: 0.7581 (m-30) REVERT: D 277 MET cc_start: 0.3570 (OUTLIER) cc_final: 0.3282 (mmp) REVERT: D 294 MET cc_start: 0.7577 (ttm) cc_final: 0.6938 (ttt) REVERT: E 103 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8368 (mttm) REVERT: E 151 GLN cc_start: 0.8818 (tt0) cc_final: 0.8474 (mt0) REVERT: G 125 ILE cc_start: 0.9601 (mp) cc_final: 0.9315 (mt) REVERT: G 129 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8841 (mtpt) REVERT: G 215 MET cc_start: 0.7884 (ttm) cc_final: 0.7665 (ttm) REVERT: G 228 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7787 (tm-30) REVERT: G 236 GLN cc_start: 0.9014 (mt0) cc_final: 0.8687 (mt0) REVERT: H 210 ASP cc_start: 0.8528 (t0) cc_final: 0.8011 (m-30) REVERT: H 294 MET cc_start: 0.7449 (ttm) cc_final: 0.6688 (ttm) REVERT: I 22 GLN cc_start: 0.8719 (mt0) cc_final: 0.8460 (mt0) REVERT: I 30 GLN cc_start: 0.7982 (tp40) cc_final: 0.6921 (tp40) REVERT: I 54 MET cc_start: 0.7847 (mtt) cc_final: 0.7149 (mtt) REVERT: I 75 ASN cc_start: 0.8913 (t0) cc_final: 0.8442 (t0) REVERT: I 139 GLU cc_start: 0.8055 (tp30) cc_final: 0.7851 (tp30) REVERT: I 141 GLN cc_start: 0.8672 (tp40) cc_final: 0.8335 (tp40) REVERT: J 21 PHE cc_start: 0.9149 (p90) cc_final: 0.8634 (p90) REVERT: J 115 GLN cc_start: 0.8792 (tm-30) cc_final: 0.7706 (tm-30) REVERT: J 118 ARG cc_start: 0.8445 (mmm160) cc_final: 0.6822 (ttp-170) REVERT: K 13 ASN cc_start: 0.8988 (m-40) cc_final: 0.8715 (m-40) REVERT: K 130 MET cc_start: 0.9035 (tpp) cc_final: 0.8773 (mpp) REVERT: K 198 ASP cc_start: 0.8270 (t0) cc_final: 0.7940 (t0) REVERT: K 204 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7548 (p90) REVERT: K 217 THR cc_start: 0.8376 (m) cc_final: 0.7417 (m) REVERT: K 224 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8765 (m) REVERT: K 225 SER cc_start: 0.9319 (t) cc_final: 0.9091 (p) REVERT: K 236 GLN cc_start: 0.8604 (mt0) cc_final: 0.8219 (mt0) REVERT: K 250 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7769 (mm-40) REVERT: L 220 MET cc_start: 0.8063 (tpp) cc_final: 0.7507 (tpp) REVERT: L 277 MET cc_start: 0.3572 (OUTLIER) cc_final: 0.3212 (mmp) REVERT: L 294 MET cc_start: 0.7199 (ttt) cc_final: 0.6972 (ttm) REVERT: L 317 GLN cc_start: 0.9485 (tt0) cc_final: 0.9231 (tm-30) REVERT: M 54 MET cc_start: 0.8105 (mtt) cc_final: 0.7691 (mtt) REVERT: M 89 GLN cc_start: 0.8893 (tt0) cc_final: 0.8646 (tt0) REVERT: M 148 ASN cc_start: 0.8499 (m-40) cc_final: 0.8107 (m-40) REVERT: N 24 GLU cc_start: 0.8281 (pt0) cc_final: 0.7865 (pm20) REVERT: N 30 GLN cc_start: 0.8089 (pm20) cc_final: 0.7771 (mm-40) REVERT: N 118 ARG cc_start: 0.8523 (mmm160) cc_final: 0.6990 (ttp-170) REVERT: O 5 GLU cc_start: 0.8509 (tp30) cc_final: 0.8155 (tp30) REVERT: O 198 ASP cc_start: 0.8176 (t0) cc_final: 0.7959 (t0) REVERT: O 204 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.6747 (p-80) REVERT: O 224 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (m) REVERT: O 229 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8821 (pp) REVERT: O 241 ASP cc_start: 0.8694 (p0) cc_final: 0.8408 (p0) REVERT: P 210 ASP cc_start: 0.7847 (t0) cc_final: 0.7415 (m-30) REVERT: P 277 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3570 (mmp) REVERT: P 294 MET cc_start: 0.7661 (ttm) cc_final: 0.6995 (ttt) REVERT: Q 103 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8330 (mttm) REVERT: Q 151 GLN cc_start: 0.8877 (tt0) cc_final: 0.8528 (mt0) REVERT: R 75 ASN cc_start: 0.8861 (t0) cc_final: 0.8535 (t0) REVERT: S 21 MET cc_start: 0.8435 (mtp) cc_final: 0.8091 (mtp) REVERT: S 125 ILE cc_start: 0.9594 (mp) cc_final: 0.9174 (mt) REVERT: S 156 ASP cc_start: 0.8646 (m-30) cc_final: 0.8327 (m-30) REVERT: S 228 GLU cc_start: 0.8128 (tt0) cc_final: 0.7539 (tm-30) REVERT: S 236 GLN cc_start: 0.8948 (mt0) cc_final: 0.8710 (mt0) REVERT: S 241 ASP cc_start: 0.8910 (p0) cc_final: 0.8551 (p0) REVERT: T 72 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7570 (tpp80) REVERT: T 210 ASP cc_start: 0.8570 (t0) cc_final: 0.8361 (m-30) REVERT: U 22 GLN cc_start: 0.8871 (mt0) cc_final: 0.8572 (mt0) REVERT: U 30 GLN cc_start: 0.7885 (tp40) cc_final: 0.7091 (tp40) REVERT: U 54 MET cc_start: 0.7818 (mtt) cc_final: 0.7289 (mtt) REVERT: U 132 LEU cc_start: 0.9155 (mt) cc_final: 0.8945 (mt) REVERT: V 21 PHE cc_start: 0.9086 (p90) cc_final: 0.8652 (p90) REVERT: V 115 GLN cc_start: 0.8832 (tm-30) cc_final: 0.7761 (tm-30) REVERT: V 118 ARG cc_start: 0.8490 (mmm160) cc_final: 0.6832 (ttp-170) REVERT: W 13 ASN cc_start: 0.8994 (m-40) cc_final: 0.8746 (m-40) REVERT: W 143 TYR cc_start: 0.8210 (m-80) cc_final: 0.8007 (m-80) REVERT: W 198 ASP cc_start: 0.8229 (t0) cc_final: 0.7893 (t0) REVERT: W 217 THR cc_start: 0.8372 (m) cc_final: 0.7464 (m) REVERT: W 224 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8822 (m) REVERT: W 225 SER cc_start: 0.9242 (t) cc_final: 0.8888 (p) REVERT: W 229 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8903 (pp) REVERT: W 236 GLN cc_start: 0.8577 (mt0) cc_final: 0.8221 (mt0) REVERT: X 80 MET cc_start: 0.8333 (ttp) cc_final: 0.7975 (ttm) REVERT: X 133 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8393 (ttmt) REVERT: X 210 ASP cc_start: 0.8058 (t0) cc_final: 0.7795 (m-30) REVERT: X 220 MET cc_start: 0.8020 (tpp) cc_final: 0.7441 (tpp) REVERT: X 317 GLN cc_start: 0.9494 (tt0) cc_final: 0.8892 (tm-30) outliers start: 149 outliers final: 112 residues processed: 814 average time/residue: 0.2065 time to fit residues: 270.0602 Evaluate side-chains 781 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 656 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 224 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 121 LYS Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 334 ILE Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 74 MET Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 275 optimal weight: 40.0000 chunk 360 optimal weight: 6.9990 chunk 415 optimal weight: 20.0000 chunk 351 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 405 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS D 53 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS P 53 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** U 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.083431 restraints weight = 63126.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085929 restraints weight = 31487.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.087595 restraints weight = 18962.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.088706 restraints weight = 12887.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.089493 restraints weight = 9501.645| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 35370 Z= 0.292 Angle : 0.665 8.443 47952 Z= 0.348 Chirality : 0.047 0.182 5244 Planarity : 0.004 0.054 6264 Dihedral : 4.974 20.632 4668 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.58 % Allowed : 21.01 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 4230 helix: 1.18 (0.17), residues: 846 sheet: -0.68 (0.14), residues: 1458 loop : -1.88 (0.12), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 134 TYR 0.041 0.002 TYR X 228 PHE 0.020 0.002 PHE R 21 TRP 0.012 0.001 TRP Q 69 HIS 0.012 0.002 HIS O 204 Details of bonding type rmsd covalent geometry : bond 0.00692 (35358) covalent geometry : angle 0.66500 (47952) hydrogen bonds : bond 0.04039 ( 1158) hydrogen bonds : angle 5.60834 ( 3438) Misc. bond : bond 0.00081 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 610 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7981 (tt0) cc_final: 0.7414 (tt0) REVERT: A 54 MET cc_start: 0.8153 (mtt) cc_final: 0.7862 (mtt) REVERT: B 54 MET cc_start: 0.9053 (mmt) cc_final: 0.8747 (mmt) REVERT: B 84 LYS cc_start: 0.9007 (mttt) cc_final: 0.8713 (mtpt) REVERT: B 118 ARG cc_start: 0.8543 (mmm160) cc_final: 0.7004 (ttp-170) REVERT: C 5 GLU cc_start: 0.8590 (tp30) cc_final: 0.8278 (tp30) REVERT: C 204 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.6860 (p-80) REVERT: C 224 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8866 (m) REVERT: C 241 ASP cc_start: 0.8812 (p0) cc_final: 0.8463 (p0) REVERT: D 210 ASP cc_start: 0.8146 (t0) cc_final: 0.7533 (m-30) REVERT: D 277 MET cc_start: 0.3609 (OUTLIER) cc_final: 0.3292 (mmp) REVERT: D 355 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8232 (m110) REVERT: E 103 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8418 (mttm) REVERT: E 151 GLN cc_start: 0.8974 (tt0) cc_final: 0.8662 (mt0) REVERT: G 125 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9298 (mt) REVERT: G 129 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8826 (mtpt) REVERT: G 236 GLN cc_start: 0.9054 (mt0) cc_final: 0.8702 (mt0) REVERT: H 210 ASP cc_start: 0.8527 (t0) cc_final: 0.8075 (m-30) REVERT: H 294 MET cc_start: 0.7690 (ttm) cc_final: 0.6976 (ttm) REVERT: I 30 GLN cc_start: 0.8166 (tp40) cc_final: 0.7168 (tp40) REVERT: I 54 MET cc_start: 0.7973 (mtt) cc_final: 0.7379 (mtt) REVERT: I 141 GLN cc_start: 0.8820 (tp40) cc_final: 0.8468 (tp40) REVERT: I 151 GLN cc_start: 0.8814 (tt0) cc_final: 0.8475 (tt0) REVERT: J 21 PHE cc_start: 0.9211 (p90) cc_final: 0.8749 (p90) REVERT: J 118 ARG cc_start: 0.8435 (mmm160) cc_final: 0.6961 (ttp-170) REVERT: K 130 MET cc_start: 0.9157 (tpp) cc_final: 0.8720 (mpp) REVERT: K 204 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.7239 (p90) REVERT: K 224 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8845 (m) REVERT: K 225 SER cc_start: 0.9315 (t) cc_final: 0.9097 (p) REVERT: K 236 GLN cc_start: 0.8653 (mt0) cc_final: 0.8226 (mt0) REVERT: L 210 ASP cc_start: 0.8187 (t0) cc_final: 0.7855 (m-30) REVERT: L 220 MET cc_start: 0.8211 (tpp) cc_final: 0.7723 (tpp) REVERT: L 277 MET cc_start: 0.3559 (OUTLIER) cc_final: 0.3135 (mmp) REVERT: M 47 GLU cc_start: 0.7985 (tt0) cc_final: 0.7403 (tt0) REVERT: M 54 MET cc_start: 0.8081 (mtt) cc_final: 0.7579 (mtt) REVERT: N 30 GLN cc_start: 0.8296 (pm20) cc_final: 0.7890 (mm-40) REVERT: N 54 MET cc_start: 0.9047 (mmt) cc_final: 0.8712 (mmt) REVERT: N 118 ARG cc_start: 0.8515 (mmm160) cc_final: 0.7013 (ttp-170) REVERT: N 132 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8917 (tp) REVERT: O 5 GLU cc_start: 0.8538 (tp30) cc_final: 0.8249 (tp30) REVERT: O 21 MET cc_start: 0.8329 (mmm) cc_final: 0.8095 (mtt) REVERT: O 204 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.6649 (p-80) REVERT: O 224 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8896 (m) REVERT: O 229 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8909 (pp) REVERT: O 241 ASP cc_start: 0.8840 (p0) cc_final: 0.8519 (p0) REVERT: P 210 ASP cc_start: 0.8121 (t0) cc_final: 0.7510 (m-30) REVERT: P 277 MET cc_start: 0.3914 (OUTLIER) cc_final: 0.3581 (mmp) REVERT: P 355 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8299 (m110) REVERT: Q 103 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8352 (mttm) REVERT: Q 151 GLN cc_start: 0.8986 (tt0) cc_final: 0.8661 (mt0) REVERT: R 8 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7950 (ttp-110) REVERT: R 129 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8522 (mp) REVERT: S 21 MET cc_start: 0.8577 (mtp) cc_final: 0.8173 (mtp) REVERT: S 125 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9248 (mt) REVERT: S 164 MET cc_start: 0.8763 (mtp) cc_final: 0.8403 (mmm) REVERT: S 203 LEU cc_start: 0.8997 (pp) cc_final: 0.8596 (pp) REVERT: S 236 GLN cc_start: 0.9016 (mt0) cc_final: 0.8739 (mt0) REVERT: S 241 ASP cc_start: 0.8973 (p0) cc_final: 0.8670 (p0) REVERT: T 69 MET cc_start: 0.8884 (pmm) cc_final: 0.8579 (pmm) REVERT: T 72 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7609 (tpp80) REVERT: U 30 GLN cc_start: 0.7921 (tp40) cc_final: 0.6898 (tp40) REVERT: U 56 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8286 (mmm-85) REVERT: U 151 GLN cc_start: 0.8952 (tt0) cc_final: 0.8618 (tt0) REVERT: V 21 PHE cc_start: 0.9291 (p90) cc_final: 0.8987 (p90) REVERT: V 118 ARG cc_start: 0.8495 (mmm160) cc_final: 0.6976 (ttp-170) REVERT: W 130 MET cc_start: 0.9287 (mpp) cc_final: 0.9020 (mtt) REVERT: W 204 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.7646 (p-80) REVERT: W 224 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8889 (m) REVERT: W 225 SER cc_start: 0.9237 (t) cc_final: 0.9022 (p) REVERT: W 236 GLN cc_start: 0.8660 (mt0) cc_final: 0.8335 (mt0) REVERT: X 210 ASP cc_start: 0.8172 (t0) cc_final: 0.7940 (m-30) REVERT: X 220 MET cc_start: 0.8187 (tpp) cc_final: 0.7689 (tpp) REVERT: X 294 MET cc_start: 0.7631 (ttt) cc_final: 0.7430 (ttm) outliers start: 172 outliers final: 136 residues processed: 740 average time/residue: 0.2063 time to fit residues: 245.1152 Evaluate side-chains 751 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 597 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 147 ASN Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 224 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 355 ASN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 121 LYS Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 186 THR Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 215 MET Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 133 LYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 334 ILE Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 127 ILE Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 176 ASP Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 292 VAL Chi-restraints excluded: chain X residue 295 VAL Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 151 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 421 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 389 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 HIS M 151 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN S 200 GLN ** U 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087573 restraints weight = 62048.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090135 restraints weight = 30527.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091806 restraints weight = 18193.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092949 restraints weight = 12261.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093755 restraints weight = 8937.206| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35370 Z= 0.142 Angle : 0.591 8.269 47952 Z= 0.305 Chirality : 0.043 0.181 5244 Planarity : 0.004 0.059 6264 Dihedral : 4.670 18.982 4668 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.47 % Allowed : 21.41 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4230 helix: 1.32 (0.17), residues: 846 sheet: -0.67 (0.14), residues: 1422 loop : -1.89 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 134 TYR 0.032 0.001 TYR X 228 PHE 0.018 0.001 PHE E 21 TRP 0.010 0.001 TRP M 162 HIS 0.012 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00333 (35358) covalent geometry : angle 0.59071 (47952) hydrogen bonds : bond 0.03466 ( 1158) hydrogen bonds : angle 5.41934 ( 3438) Misc. bond : bond 0.00046 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 643 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7972 (tt0) cc_final: 0.7364 (tt0) REVERT: A 54 MET cc_start: 0.7991 (mtt) cc_final: 0.7299 (mtt) REVERT: A 89 GLN cc_start: 0.9083 (tt0) cc_final: 0.8713 (tt0) REVERT: B 54 MET cc_start: 0.8884 (mmt) cc_final: 0.8489 (mmt) REVERT: B 84 LYS cc_start: 0.8970 (mttt) cc_final: 0.8667 (mtpt) REVERT: B 118 ARG cc_start: 0.8466 (mmm160) cc_final: 0.6936 (ttp-170) REVERT: C 5 GLU cc_start: 0.8552 (tp30) cc_final: 0.8255 (tp30) REVERT: C 198 ASP cc_start: 0.8227 (t0) cc_final: 0.7957 (t0) REVERT: C 204 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.6115 (p90) REVERT: C 241 ASP cc_start: 0.8692 (p0) cc_final: 0.8407 (p0) REVERT: D 69 MET cc_start: 0.8661 (pmm) cc_final: 0.7820 (pmm) REVERT: D 210 ASP cc_start: 0.8266 (t0) cc_final: 0.7713 (m-30) REVERT: D 220 MET cc_start: 0.8664 (tpt) cc_final: 0.8402 (tpt) REVERT: D 277 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3290 (mmp) REVERT: D 294 MET cc_start: 0.7649 (ttm) cc_final: 0.6986 (ttt) REVERT: E 103 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8389 (mttm) REVERT: E 151 GLN cc_start: 0.8896 (tt0) cc_final: 0.8612 (mt0) REVERT: F 8 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8007 (ttp80) REVERT: G 125 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9312 (mt) REVERT: G 228 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: G 236 GLN cc_start: 0.9026 (mt0) cc_final: 0.8689 (mt0) REVERT: H 69 MET cc_start: 0.8755 (pmm) cc_final: 0.8504 (pmm) REVERT: H 210 ASP cc_start: 0.8620 (t0) cc_final: 0.8376 (m-30) REVERT: H 294 MET cc_start: 0.7591 (ttm) cc_final: 0.6803 (ttm) REVERT: I 22 GLN cc_start: 0.8771 (mt0) cc_final: 0.8521 (mt0) REVERT: I 30 GLN cc_start: 0.8074 (tp40) cc_final: 0.6988 (tp40) REVERT: I 47 GLU cc_start: 0.7904 (tt0) cc_final: 0.7556 (tt0) REVERT: I 141 GLN cc_start: 0.8715 (tp40) cc_final: 0.8355 (tp40) REVERT: J 21 PHE cc_start: 0.9180 (p90) cc_final: 0.8694 (p90) REVERT: J 118 ARG cc_start: 0.8402 (mmm160) cc_final: 0.6946 (ttp-170) REVERT: K 13 ASN cc_start: 0.9038 (m-40) cc_final: 0.8768 (m-40) REVERT: K 130 MET cc_start: 0.9059 (tpp) cc_final: 0.8839 (mpp) REVERT: K 198 ASP cc_start: 0.7914 (t0) cc_final: 0.7547 (t0) REVERT: K 204 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8261 (p-80) REVERT: K 217 THR cc_start: 0.8455 (m) cc_final: 0.7744 (m) REVERT: K 224 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8817 (m) REVERT: K 225 SER cc_start: 0.9315 (t) cc_final: 0.9084 (p) REVERT: K 236 GLN cc_start: 0.8623 (mt0) cc_final: 0.8216 (mt0) REVERT: L 69 MET cc_start: 0.8505 (pmm) cc_final: 0.8107 (pmm) REVERT: L 210 ASP cc_start: 0.8106 (t0) cc_final: 0.7843 (m-30) REVERT: L 277 MET cc_start: 0.3533 (OUTLIER) cc_final: 0.3129 (mmp) REVERT: L 317 GLN cc_start: 0.9502 (tt0) cc_final: 0.9174 (tm-30) REVERT: M 47 GLU cc_start: 0.7964 (tt0) cc_final: 0.7358 (tt0) REVERT: M 54 MET cc_start: 0.8139 (mtt) cc_final: 0.7748 (mtt) REVERT: M 89 GLN cc_start: 0.9077 (tt0) cc_final: 0.8733 (tt0) REVERT: N 30 GLN cc_start: 0.8030 (pm20) cc_final: 0.7746 (mm-40) REVERT: N 54 MET cc_start: 0.8898 (mmt) cc_final: 0.8448 (mmt) REVERT: N 118 ARG cc_start: 0.8515 (mmm160) cc_final: 0.6934 (ttp-170) REVERT: O 5 GLU cc_start: 0.8555 (tp30) cc_final: 0.8272 (tp30) REVERT: O 198 ASP cc_start: 0.8361 (t0) cc_final: 0.7918 (t0) REVERT: O 204 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.6624 (p-80) REVERT: O 229 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8855 (pp) REVERT: O 241 ASP cc_start: 0.8639 (p0) cc_final: 0.8434 (p0) REVERT: P 210 ASP cc_start: 0.8172 (t0) cc_final: 0.7655 (m-30) REVERT: P 277 MET cc_start: 0.3879 (OUTLIER) cc_final: 0.3580 (mmp) REVERT: P 294 MET cc_start: 0.7621 (ttm) cc_final: 0.6976 (ttt) REVERT: P 355 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8174 (m110) REVERT: Q 103 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8418 (mttm) REVERT: Q 151 GLN cc_start: 0.8931 (tt0) cc_final: 0.8631 (mt0) REVERT: S 21 MET cc_start: 0.8482 (mtp) cc_final: 0.8102 (mtp) REVERT: S 125 ILE cc_start: 0.9565 (mp) cc_final: 0.9137 (mt) REVERT: S 203 LEU cc_start: 0.8945 (pp) cc_final: 0.8552 (pp) REVERT: S 228 GLU cc_start: 0.8106 (tt0) cc_final: 0.7470 (tm-30) REVERT: S 236 GLN cc_start: 0.8993 (mt0) cc_final: 0.8746 (mt0) REVERT: S 241 ASP cc_start: 0.8927 (p0) cc_final: 0.8580 (p0) REVERT: T 69 MET cc_start: 0.8864 (pmm) cc_final: 0.8540 (pmm) REVERT: T 72 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7532 (ttm-80) REVERT: U 30 GLN cc_start: 0.7916 (tp40) cc_final: 0.6939 (tp40) REVERT: U 47 GLU cc_start: 0.7947 (tt0) cc_final: 0.7563 (tt0) REVERT: U 151 GLN cc_start: 0.8792 (tt0) cc_final: 0.8506 (tt0) REVERT: V 21 PHE cc_start: 0.9205 (p90) cc_final: 0.8892 (p90) REVERT: V 118 ARG cc_start: 0.8449 (mmm160) cc_final: 0.6955 (ttp-170) REVERT: W 13 ASN cc_start: 0.9051 (m-40) cc_final: 0.8794 (m-40) REVERT: W 198 ASP cc_start: 0.7898 (t0) cc_final: 0.7535 (t0) REVERT: W 204 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7621 (p90) REVERT: W 224 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8840 (m) REVERT: W 225 SER cc_start: 0.9179 (t) cc_final: 0.8787 (p) REVERT: W 229 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8816 (pp) REVERT: W 236 GLN cc_start: 0.8632 (mt0) cc_final: 0.8336 (mt0) REVERT: W 250 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7619 (mm-40) REVERT: X 69 MET cc_start: 0.8593 (pmm) cc_final: 0.7906 (pmm) REVERT: X 210 ASP cc_start: 0.8037 (t0) cc_final: 0.7821 (m-30) REVERT: X 220 MET cc_start: 0.8037 (tpp) cc_final: 0.7489 (tpp) REVERT: X 317 GLN cc_start: 0.9509 (tt0) cc_final: 0.8872 (tm-30) outliers start: 168 outliers final: 127 residues processed: 765 average time/residue: 0.2014 time to fit residues: 249.4047 Evaluate side-chains 764 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 623 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 355 ASN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 176 ASP Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 210 ASP Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 334 ILE Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 176 ASP Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 204 HIS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 310 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 13 optimal weight: 0.9990 chunk 344 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 409 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 395 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 151 GLN C 200 GLN C 204 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN G 200 GLN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 HIS N 59 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN S 200 GLN ** U 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089337 restraints weight = 61541.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091941 restraints weight = 30314.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093646 restraints weight = 18005.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094788 restraints weight = 12042.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095546 restraints weight = 8760.469| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35370 Z= 0.121 Angle : 0.585 8.186 47952 Z= 0.299 Chirality : 0.043 0.212 5244 Planarity : 0.004 0.057 6264 Dihedral : 4.518 18.015 4668 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.83 % Allowed : 22.28 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.12), residues: 4230 helix: 1.27 (0.18), residues: 858 sheet: -0.52 (0.14), residues: 1380 loop : -1.95 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 134 TYR 0.028 0.001 TYR X 228 PHE 0.029 0.001 PHE R 21 TRP 0.011 0.001 TRP T 209 HIS 0.009 0.001 HIS O 204 Details of bonding type rmsd covalent geometry : bond 0.00281 (35358) covalent geometry : angle 0.58482 (47952) hydrogen bonds : bond 0.03329 ( 1158) hydrogen bonds : angle 5.30694 ( 3438) Misc. bond : bond 0.00040 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 657 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9059 (tt0) cc_final: 0.8684 (tt0) REVERT: B 54 MET cc_start: 0.8777 (mmt) cc_final: 0.8412 (mmt) REVERT: B 84 LYS cc_start: 0.8935 (mttt) cc_final: 0.8670 (mtpt) REVERT: B 118 ARG cc_start: 0.8477 (mmm160) cc_final: 0.6929 (ttp-170) REVERT: C 5 GLU cc_start: 0.8545 (tp30) cc_final: 0.8206 (tp30) REVERT: C 198 ASP cc_start: 0.8201 (t0) cc_final: 0.7877 (t0) REVERT: C 204 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.6818 (p-80) REVERT: C 241 ASP cc_start: 0.8705 (p0) cc_final: 0.8414 (p0) REVERT: D 69 MET cc_start: 0.8627 (pmm) cc_final: 0.7737 (pmm) REVERT: D 210 ASP cc_start: 0.8238 (t0) cc_final: 0.7691 (m-30) REVERT: D 220 MET cc_start: 0.8473 (tpt) cc_final: 0.8197 (tpt) REVERT: D 277 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.3287 (mmp) REVERT: D 294 MET cc_start: 0.7572 (ttm) cc_final: 0.6930 (ttt) REVERT: E 28 LEU cc_start: 0.9179 (mt) cc_final: 0.8871 (mm) REVERT: E 103 LYS cc_start: 0.8905 (mmtp) cc_final: 0.8431 (mttm) REVERT: E 151 GLN cc_start: 0.8851 (tt0) cc_final: 0.8458 (mt0) REVERT: F 8 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8019 (ttp80) REVERT: F 141 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7993 (mm-40) REVERT: G 125 ILE cc_start: 0.9585 (mp) cc_final: 0.9289 (mt) REVERT: G 228 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: G 236 GLN cc_start: 0.9055 (mt0) cc_final: 0.8782 (mt0) REVERT: H 210 ASP cc_start: 0.8550 (t0) cc_final: 0.8305 (m-30) REVERT: H 294 MET cc_start: 0.7397 (ttm) cc_final: 0.6605 (ttm) REVERT: I 30 GLN cc_start: 0.8064 (tp40) cc_final: 0.7118 (tp40) REVERT: I 47 GLU cc_start: 0.7878 (tt0) cc_final: 0.7516 (tt0) REVERT: I 141 GLN cc_start: 0.8693 (tp40) cc_final: 0.8288 (tp40) REVERT: I 151 GLN cc_start: 0.8599 (tt0) cc_final: 0.8376 (tt0) REVERT: J 21 PHE cc_start: 0.9150 (p90) cc_final: 0.8731 (p90) REVERT: J 35 GLN cc_start: 0.9125 (mt0) cc_final: 0.8700 (tt0) REVERT: J 118 ARG cc_start: 0.8439 (mmm160) cc_final: 0.6830 (ttp-170) REVERT: K 13 ASN cc_start: 0.9053 (m-40) cc_final: 0.8779 (m-40) REVERT: K 22 PHE cc_start: 0.8913 (p90) cc_final: 0.8649 (p90) REVERT: K 130 MET cc_start: 0.9036 (tpp) cc_final: 0.8733 (mpp) REVERT: K 198 ASP cc_start: 0.7684 (t0) cc_final: 0.7424 (t0) REVERT: K 224 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8773 (m) REVERT: K 225 SER cc_start: 0.9281 (t) cc_final: 0.8894 (p) REVERT: K 236 GLN cc_start: 0.8588 (mt0) cc_final: 0.8184 (mt0) REVERT: K 250 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7841 (mm-40) REVERT: L 69 MET cc_start: 0.8551 (pmm) cc_final: 0.7910 (pmm) REVERT: L 80 MET cc_start: 0.8177 (ttp) cc_final: 0.7794 (ttm) REVERT: L 210 ASP cc_start: 0.8033 (t0) cc_final: 0.7767 (m-30) REVERT: L 220 MET cc_start: 0.8368 (tpt) cc_final: 0.7940 (tpp) REVERT: L 277 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3358 (mmp) REVERT: L 317 GLN cc_start: 0.9476 (tt0) cc_final: 0.9195 (tm-30) REVERT: M 54 MET cc_start: 0.8089 (mtt) cc_final: 0.7716 (mtt) REVERT: M 89 GLN cc_start: 0.9008 (tt0) cc_final: 0.8686 (tt0) REVERT: N 30 GLN cc_start: 0.7934 (pm20) cc_final: 0.7724 (mm-40) REVERT: N 54 MET cc_start: 0.8794 (mmt) cc_final: 0.8347 (mmt) REVERT: N 118 ARG cc_start: 0.8499 (mmm160) cc_final: 0.6935 (ttp-170) REVERT: N 132 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8967 (tp) REVERT: O 5 GLU cc_start: 0.8558 (tp30) cc_final: 0.8225 (tp30) REVERT: O 198 ASP cc_start: 0.8286 (t0) cc_final: 0.7766 (t0) REVERT: O 204 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.6515 (p90) REVERT: O 229 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8633 (pp) REVERT: P 69 MET cc_start: 0.8324 (pmm) cc_final: 0.7782 (pmm) REVERT: P 210 ASP cc_start: 0.8249 (t0) cc_final: 0.7720 (m-30) REVERT: P 277 MET cc_start: 0.3849 (OUTLIER) cc_final: 0.3578 (mmp) REVERT: P 294 MET cc_start: 0.7553 (ttm) cc_final: 0.6903 (ttt) REVERT: P 355 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8115 (m110) REVERT: Q 103 LYS cc_start: 0.8882 (mmtp) cc_final: 0.8406 (mttm) REVERT: Q 151 GLN cc_start: 0.8938 (tt0) cc_final: 0.8539 (mt0) REVERT: S 21 MET cc_start: 0.8516 (mtp) cc_final: 0.8124 (mtp) REVERT: S 125 ILE cc_start: 0.9538 (mp) cc_final: 0.9097 (mt) REVERT: S 129 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8831 (mtpt) REVERT: S 134 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8345 (ptp-110) REVERT: S 156 ASP cc_start: 0.8445 (m-30) cc_final: 0.8218 (m-30) REVERT: S 228 GLU cc_start: 0.7984 (tt0) cc_final: 0.7401 (tm-30) REVERT: S 241 ASP cc_start: 0.8796 (p0) cc_final: 0.8479 (p0) REVERT: T 69 MET cc_start: 0.8845 (pmm) cc_final: 0.8516 (pmm) REVERT: U 22 GLN cc_start: 0.8838 (mt0) cc_final: 0.8550 (mt0) REVERT: U 30 GLN cc_start: 0.7892 (tp40) cc_final: 0.6915 (tp40) REVERT: U 47 GLU cc_start: 0.7921 (tt0) cc_final: 0.7516 (tt0) REVERT: V 21 PHE cc_start: 0.9140 (p90) cc_final: 0.8849 (p90) REVERT: V 118 ARG cc_start: 0.8483 (mmm160) cc_final: 0.7157 (tmm160) REVERT: W 13 ASN cc_start: 0.9054 (m-40) cc_final: 0.8801 (m-40) REVERT: W 198 ASP cc_start: 0.7758 (t0) cc_final: 0.7484 (t0) REVERT: W 224 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8830 (m) REVERT: W 225 SER cc_start: 0.9163 (t) cc_final: 0.8218 (p) REVERT: W 229 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8799 (pp) REVERT: W 236 GLN cc_start: 0.8604 (mt0) cc_final: 0.8261 (mt0) REVERT: W 250 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7577 (mm-40) REVERT: X 69 MET cc_start: 0.8600 (pmm) cc_final: 0.8035 (pmm) REVERT: X 210 ASP cc_start: 0.7986 (t0) cc_final: 0.7763 (m-30) REVERT: X 317 GLN cc_start: 0.9472 (tt0) cc_final: 0.8907 (tm-30) outliers start: 144 outliers final: 113 residues processed: 761 average time/residue: 0.1990 time to fit residues: 244.9505 Evaluate side-chains 756 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 631 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 355 ASN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 210 ASP Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 334 ILE Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 292 VAL Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 343 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 294 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 418 optimal weight: 0.0060 chunk 277 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 250 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS O 250 GLN ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** U 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.088351 restraints weight = 61870.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090949 restraints weight = 30550.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092655 restraints weight = 18112.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.093795 restraints weight = 12126.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094561 restraints weight = 8801.777| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35370 Z= 0.140 Angle : 0.594 10.656 47952 Z= 0.305 Chirality : 0.043 0.183 5244 Planarity : 0.004 0.062 6264 Dihedral : 4.525 18.862 4668 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.73 % Allowed : 22.71 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 4230 helix: 1.28 (0.18), residues: 858 sheet: -0.53 (0.14), residues: 1380 loop : -1.95 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 134 TYR 0.028 0.001 TYR X 228 PHE 0.015 0.001 PHE B 53 TRP 0.012 0.001 TRP T 209 HIS 0.008 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00329 (35358) covalent geometry : angle 0.59361 (47952) hydrogen bonds : bond 0.03343 ( 1158) hydrogen bonds : angle 5.29305 ( 3438) Misc. bond : bond 0.00044 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8460 Ramachandran restraints generated. 4230 Oldfield, 0 Emsley, 4230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 638 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.9070 (tt0) cc_final: 0.8700 (tt0) REVERT: B 54 MET cc_start: 0.8765 (mmt) cc_final: 0.8374 (mmt) REVERT: B 59 ASN cc_start: 0.9142 (m-40) cc_final: 0.8641 (m110) REVERT: B 84 LYS cc_start: 0.8945 (mttt) cc_final: 0.8676 (mtpt) REVERT: B 118 ARG cc_start: 0.8468 (mmm160) cc_final: 0.6924 (ttp-170) REVERT: B 141 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7508 (mm-40) REVERT: C 5 GLU cc_start: 0.8537 (tp30) cc_final: 0.8188 (tp30) REVERT: C 198 ASP cc_start: 0.8290 (t0) cc_final: 0.8009 (t0) REVERT: C 204 HIS cc_start: 0.9032 (OUTLIER) cc_final: 0.7045 (p-80) REVERT: C 241 ASP cc_start: 0.8722 (p0) cc_final: 0.8431 (p0) REVERT: D 69 MET cc_start: 0.8636 (pmm) cc_final: 0.7743 (pmm) REVERT: D 210 ASP cc_start: 0.8274 (t0) cc_final: 0.7726 (m-30) REVERT: D 220 MET cc_start: 0.8525 (tpt) cc_final: 0.8236 (tpt) REVERT: D 277 MET cc_start: 0.3526 (OUTLIER) cc_final: 0.3287 (mmp) REVERT: D 294 MET cc_start: 0.7618 (ttm) cc_final: 0.6969 (ttt) REVERT: E 28 LEU cc_start: 0.9201 (mt) cc_final: 0.8876 (mm) REVERT: E 54 MET cc_start: 0.7761 (mtt) cc_final: 0.7097 (mtt) REVERT: E 103 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8430 (mttm) REVERT: E 151 GLN cc_start: 0.8857 (tt0) cc_final: 0.8431 (mt0) REVERT: F 8 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8058 (ttp80) REVERT: G 13 ASN cc_start: 0.8770 (m-40) cc_final: 0.8188 (m110) REVERT: G 125 ILE cc_start: 0.9579 (mp) cc_final: 0.9292 (mt) REVERT: G 134 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8444 (ptp-110) REVERT: G 164 MET cc_start: 0.8853 (mmm) cc_final: 0.8608 (ttm) REVERT: G 203 LEU cc_start: 0.8992 (pp) cc_final: 0.8649 (pp) REVERT: G 228 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: G 236 GLN cc_start: 0.9068 (mt0) cc_final: 0.8768 (mt0) REVERT: H 69 MET cc_start: 0.8706 (pmm) cc_final: 0.8470 (pmm) REVERT: H 210 ASP cc_start: 0.8575 (t0) cc_final: 0.8335 (m-30) REVERT: H 294 MET cc_start: 0.7454 (ttm) cc_final: 0.6681 (ttm) REVERT: I 30 GLN cc_start: 0.8071 (tp40) cc_final: 0.7080 (tp40) REVERT: I 47 GLU cc_start: 0.7873 (tt0) cc_final: 0.7491 (tt0) REVERT: I 141 GLN cc_start: 0.8704 (tp40) cc_final: 0.8286 (tp40) REVERT: I 151 GLN cc_start: 0.8478 (tt0) cc_final: 0.8272 (tt0) REVERT: J 21 PHE cc_start: 0.9169 (p90) cc_final: 0.8722 (p90) REVERT: J 35 GLN cc_start: 0.9126 (mt0) cc_final: 0.8694 (tt0) REVERT: J 118 ARG cc_start: 0.8441 (mmm160) cc_final: 0.6825 (ttp-170) REVERT: K 13 ASN cc_start: 0.9047 (m-40) cc_final: 0.8776 (m-40) REVERT: K 130 MET cc_start: 0.9020 (tpp) cc_final: 0.8631 (mpp) REVERT: K 224 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8799 (m) REVERT: K 225 SER cc_start: 0.9278 (t) cc_final: 0.8840 (p) REVERT: K 236 GLN cc_start: 0.8573 (mt0) cc_final: 0.8157 (mt0) REVERT: L 69 MET cc_start: 0.8582 (pmm) cc_final: 0.7989 (pmm) REVERT: L 80 MET cc_start: 0.8183 (ttp) cc_final: 0.7754 (ttm) REVERT: L 210 ASP cc_start: 0.8045 (t0) cc_final: 0.7805 (m-30) REVERT: L 220 MET cc_start: 0.8366 (tpt) cc_final: 0.7939 (tpp) REVERT: L 277 MET cc_start: 0.3719 (OUTLIER) cc_final: 0.3371 (mmp) REVERT: L 317 GLN cc_start: 0.9551 (tt0) cc_final: 0.8886 (tm-30) REVERT: M 47 GLU cc_start: 0.7949 (tt0) cc_final: 0.7348 (tt0) REVERT: M 54 MET cc_start: 0.8041 (mtt) cc_final: 0.7607 (mtt) REVERT: M 89 GLN cc_start: 0.9018 (tt0) cc_final: 0.8699 (tt0) REVERT: N 30 GLN cc_start: 0.7953 (pm20) cc_final: 0.7718 (mm-40) REVERT: N 118 ARG cc_start: 0.8451 (mmm160) cc_final: 0.6926 (ttp-170) REVERT: N 132 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8975 (tp) REVERT: O 5 GLU cc_start: 0.8553 (tp30) cc_final: 0.8204 (tp30) REVERT: O 204 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.6871 (p-80) REVERT: O 229 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8799 (pp) REVERT: P 69 MET cc_start: 0.8286 (pmm) cc_final: 0.7737 (pmm) REVERT: P 80 MET cc_start: 0.7934 (ttm) cc_final: 0.7577 (ttm) REVERT: P 210 ASP cc_start: 0.8287 (t0) cc_final: 0.7759 (m-30) REVERT: P 277 MET cc_start: 0.3838 (OUTLIER) cc_final: 0.3576 (mmp) REVERT: P 294 MET cc_start: 0.7585 (ttm) cc_final: 0.6916 (ttt) REVERT: Q 54 MET cc_start: 0.7683 (mtt) cc_final: 0.6911 (mtt) REVERT: Q 103 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8422 (mttm) REVERT: Q 151 GLN cc_start: 0.8921 (tt0) cc_final: 0.8472 (mt0) REVERT: S 21 MET cc_start: 0.8494 (mtp) cc_final: 0.8100 (mtp) REVERT: S 125 ILE cc_start: 0.9531 (mp) cc_final: 0.9113 (mt) REVERT: S 129 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8646 (tmmt) REVERT: S 241 ASP cc_start: 0.8799 (p0) cc_final: 0.8492 (p0) REVERT: T 69 MET cc_start: 0.8844 (pmm) cc_final: 0.8538 (pmm) REVERT: T 210 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: U 22 GLN cc_start: 0.8880 (mt0) cc_final: 0.8587 (mt0) REVERT: U 30 GLN cc_start: 0.7974 (tp40) cc_final: 0.7056 (tp40) REVERT: U 47 GLU cc_start: 0.7924 (tt0) cc_final: 0.7499 (tt0) REVERT: V 21 PHE cc_start: 0.9173 (p90) cc_final: 0.8860 (p90) REVERT: V 35 GLN cc_start: 0.9097 (mt0) cc_final: 0.8701 (tt0) REVERT: V 118 ARG cc_start: 0.8488 (mmm160) cc_final: 0.7163 (tmm160) REVERT: W 13 ASN cc_start: 0.9044 (m-40) cc_final: 0.8786 (m-40) REVERT: W 224 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8798 (m) REVERT: W 225 SER cc_start: 0.9161 (t) cc_final: 0.8161 (p) REVERT: W 229 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8797 (pp) REVERT: W 236 GLN cc_start: 0.8596 (mt0) cc_final: 0.8246 (mt0) REVERT: W 250 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7729 (mm-40) REVERT: X 69 MET cc_start: 0.8603 (pmm) cc_final: 0.8050 (pmm) REVERT: X 210 ASP cc_start: 0.8001 (t0) cc_final: 0.7785 (m-30) REVERT: X 220 MET cc_start: 0.8374 (tpt) cc_final: 0.7899 (tpp) outliers start: 140 outliers final: 121 residues processed: 743 average time/residue: 0.2033 time to fit residues: 244.2748 Evaluate side-chains 759 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 626 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 310 ILE Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 334 ILE Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 277 MET Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 199 ILE Chi-restraints excluded: chain S residue 204 HIS Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 210 ASP Chi-restraints excluded: chain T residue 212 THR Chi-restraints excluded: chain T residue 334 ILE Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 211 LEU Chi-restraints excluded: chain X residue 212 THR Chi-restraints excluded: chain X residue 223 ILE Chi-restraints excluded: chain X residue 292 VAL Chi-restraints excluded: chain X residue 319 ILE Chi-restraints excluded: chain X residue 334 ILE Chi-restraints excluded: chain X residue 343 THR Chi-restraints excluded: chain X residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 355 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 185 optimal weight: 0.3980 chunk 279 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 chunk 349 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 204 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN G 200 GLN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN O 204 HIS ** P 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.085418 restraints weight = 62440.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.087946 restraints weight = 31040.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.089601 restraints weight = 18601.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090722 restraints weight = 12544.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091483 restraints weight = 9185.984| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 35370 Z= 0.239 Angle : 0.648 10.076 47952 Z= 0.336 Chirality : 0.046 0.198 5244 Planarity : 0.004 0.067 6264 Dihedral : 4.819 20.330 4668 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.37 % Allowed : 22.23 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4230 helix: 1.24 (0.17), residues: 846 sheet: -0.77 (0.13), residues: 1476 loop : -1.86 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 134 TYR 0.030 0.002 TYR X 228 PHE 0.018 0.002 PHE R 21 TRP 0.011 0.001 TRP I 162 HIS 0.012 0.002 HIS O 204 Details of bonding type rmsd covalent geometry : bond 0.00567 (35358) covalent geometry : angle 0.64828 (47952) hydrogen bonds : bond 0.03728 ( 1158) hydrogen bonds : angle 5.45192 ( 3438) Misc. bond : bond 0.00068 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5900.26 seconds wall clock time: 102 minutes 32.63 seconds (6152.63 seconds total)