Starting phenix.real_space_refine on Sat Aug 8 05:30:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.map" model { file = "/net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wgb_65952/08_2026/9wgb_65952.cif" } resolution = 3.6 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= 0.003 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 128 5.16 5 C 16368 2.51 5 N 4240 2.21 5 O 5152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25888 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "B" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "D" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "F" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "G" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "H" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "I" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "J" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "K" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "L" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "M" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "N" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "O" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Chain: "P" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1618 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Time building chain proxies: 6.31, per 1000 atoms: 0.24 Number of scatterers: 25888 At special positions: 0 Unit cell: (159.36, 159.36, 103.75, 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 128 16.00 O 5152 8.00 N 4240 7.00 C 16368 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=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6368 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 46 sheets defined 24.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 107 through 124 removed outlier: 4.346A pdb=" N TYR A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.887A pdb=" N GLN B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 4.412A pdb=" N TYR B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.540A pdb=" N ARG B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.597A pdb=" N GLN C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 124 removed outlier: 4.381A pdb=" N TYR C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.509A pdb=" N ARG C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.604A pdb=" N GLN D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 removed outlier: 4.324A pdb=" N TYR D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.648A pdb=" N ARG D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 Processing helix chain 'E' and resid 64 through 70 removed outlier: 3.547A pdb=" N GLN E 70 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 removed outlier: 4.414A pdb=" N TYR E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'F' and resid 24 through 36 Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.648A pdb=" N GLN F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 removed outlier: 4.393A pdb=" N TYR F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.566A pdb=" N ARG F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 36 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 107 through 124 removed outlier: 4.333A pdb=" N TYR G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 132 Processing helix chain 'G' and resid 176 through 183 Processing helix chain 'H' and resid 24 through 36 Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.728A pdb=" N GLN H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 124 removed outlier: 4.425A pdb=" N TYR H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.640A pdb=" N ARG H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 36 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 107 through 124 removed outlier: 4.380A pdb=" N TYR I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 176 through 183 removed outlier: 3.509A pdb=" N ARG I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 36 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.602A pdb=" N GLN J 70 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 124 removed outlier: 4.420A pdb=" N TYR J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'J' and resid 176 through 183 removed outlier: 3.599A pdb=" N ARG J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 36 Processing helix chain 'K' and resid 64 through 70 removed outlier: 3.554A pdb=" N GLN K 70 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 124 removed outlier: 4.370A pdb=" N TYR K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 132 Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.503A pdb=" N ARG K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 36 Processing helix chain 'L' and resid 64 through 70 removed outlier: 3.527A pdb=" N GLN L 70 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 124 removed outlier: 4.404A pdb=" N TYR L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 132 Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.572A pdb=" N ARG L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 36 Processing helix chain 'M' and resid 64 through 70 removed outlier: 3.523A pdb=" N GLN M 70 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 124 removed outlier: 4.377A pdb=" N TYR M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.588A pdb=" N ARG M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 36 Processing helix chain 'N' and resid 64 through 70 removed outlier: 3.814A pdb=" N GLN N 70 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 124 removed outlier: 4.417A pdb=" N TYR N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 132 Processing helix chain 'N' and resid 176 through 183 removed outlier: 3.678A pdb=" N ARG N 183 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 36 Processing helix chain 'O' and resid 64 through 70 removed outlier: 3.642A pdb=" N GLN O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 124 removed outlier: 4.370A pdb=" N TYR O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 132 Processing helix chain 'O' and resid 176 through 183 removed outlier: 3.505A pdb=" N ARG O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 36 Processing helix chain 'P' and resid 64 through 70 removed outlier: 3.845A pdb=" N GLN P 70 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 124 removed outlier: 4.377A pdb=" N TYR P 111 " --> pdb=" O SER P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 Processing helix chain 'P' and resid 176 through 183 removed outlier: 3.602A pdb=" N ARG P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 3.525A pdb=" N TYR A 45 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 49 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 7.137A pdb=" N GLU A 79 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 106 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET A 77 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA A 188 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 215 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 190 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 213 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 192 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS A 211 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA A 209 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL A 196 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.646A pdb=" N VAL A 223 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.355A pdb=" N TYR B 45 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 62 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 49 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.948A pdb=" N GLU B 79 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA B 106 " --> pdb=" O MET B 77 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 77 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N LEU B 187 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP B 216 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 212 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 193 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 210 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 195 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE B 208 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 197 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 206 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.665A pdb=" N VAL B 223 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 50 removed outlier: 3.567A pdb=" N TYR C 45 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 49 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 151 removed outlier: 7.121A pdb=" N GLU C 79 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA C 106 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET C 77 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA C 188 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 215 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 190 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 213 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 192 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS C 211 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA C 209 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 196 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.590A pdb=" N VAL C 223 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 50 removed outlier: 3.684A pdb=" N ASN D 49 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 149 through 151 removed outlier: 7.117A pdb=" N GLU D 79 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA D 106 " --> pdb=" O MET D 77 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET D 77 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA D 188 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE D 215 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA D 190 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU D 213 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE D 192 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS D 211 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA D 209 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 196 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.620A pdb=" N VAL D 223 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 43 through 50 removed outlier: 3.581A pdb=" N TYR E 45 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 49 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 149 through 151 removed outlier: 7.066A pdb=" N GLU E 79 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA E 106 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET E 77 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA E 188 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE E 215 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA E 190 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU E 213 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE E 192 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS E 211 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA E 209 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 196 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 171 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER E 163 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 223 through 224 removed outlier: 3.668A pdb=" N VAL E 223 " --> pdb=" O GLU E 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 43 through 50 removed outlier: 3.527A pdb=" N TYR F 45 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN F 49 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 58 " --> pdb=" O ASN F 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 149 through 151 removed outlier: 7.102A pdb=" N GLU F 79 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA F 106 " --> pdb=" O MET F 77 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET F 77 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA F 188 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE F 215 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA F 190 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 213 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE F 192 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS F 211 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA F 209 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL F 196 " --> pdb=" O THR F 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 213 " --> pdb=" O MET F 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 223 through 224 removed outlier: 3.595A pdb=" N VAL F 223 " --> pdb=" O GLU F 231 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 43 through 50 removed outlier: 3.599A pdb=" N TYR G 45 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 49 " --> pdb=" O SER G 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 149 through 151 removed outlier: 7.120A pdb=" N GLU G 79 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA G 106 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET G 77 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA G 188 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE G 215 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA G 190 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU G 213 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE G 192 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS G 211 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA G 209 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL G 196 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG G 171 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 223 through 224 removed outlier: 3.656A pdb=" N VAL G 223 " --> pdb=" O GLU G 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 43 through 50 removed outlier: 3.547A pdb=" N TYR H 45 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN H 49 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 149 through 151 removed outlier: 6.933A pdb=" N GLU H 79 " --> pdb=" O THR H 104 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA H 106 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET H 77 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA H 188 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE H 215 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA H 190 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU H 213 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE H 192 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS H 211 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA H 209 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL H 196 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU H 213 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER H 163 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 223 through 224 removed outlier: 3.652A pdb=" N VAL H 223 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 45 through 50 removed outlier: 3.738A pdb=" N ASN I 49 " --> pdb=" O SER I 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 149 through 151 removed outlier: 7.093A pdb=" N GLU I 79 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA I 106 " --> pdb=" O MET I 77 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET I 77 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA I 188 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE I 215 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA I 190 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU I 213 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE I 192 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS I 211 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA I 209 " --> pdb=" O PRO I 194 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL I 196 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 213 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER I 163 " --> pdb=" O SER I 167 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 223 through 224 removed outlier: 3.659A pdb=" N VAL I 223 " --> pdb=" O GLU I 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 43 through 50 removed outlier: 4.083A pdb=" N TYR J 45 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS J 62 " --> pdb=" O TYR J 45 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN J 49 " --> pdb=" O SER J 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 149 through 151 removed outlier: 6.914A pdb=" N GLU J 79 " --> pdb=" O THR J 104 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA J 106 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET J 77 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA J 188 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE J 215 " --> pdb=" O ALA J 188 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA J 190 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU J 213 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE J 192 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS J 211 " --> pdb=" O ILE J 192 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA J 209 " --> pdb=" O PRO J 194 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL J 196 " --> pdb=" O THR J 207 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU J 213 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 162 " --> pdb=" O ILE J 215 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 43 through 50 removed outlier: 3.681A pdb=" N ASN K 49 " --> pdb=" O SER K 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 149 through 151 removed outlier: 7.102A pdb=" N GLU K 79 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA K 106 " --> pdb=" O MET K 77 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET K 77 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA K 188 " --> pdb=" O ILE K 215 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE K 215 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA K 190 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU K 213 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE K 192 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS K 211 " --> pdb=" O ILE K 192 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA K 209 " --> pdb=" O PRO K 194 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL K 196 " --> pdb=" O THR K 207 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER K 163 " --> pdb=" O SER K 167 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 43 through 50 removed outlier: 3.572A pdb=" N TYR L 45 " --> pdb=" O LYS L 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN L 49 " --> pdb=" O SER L 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 149 through 151 removed outlier: 7.077A pdb=" N GLU L 79 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA L 106 " --> pdb=" O MET L 77 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET L 77 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N LEU L 187 " --> pdb=" O ASP L 216 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP L 216 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS L 212 " --> pdb=" O ILE L 191 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR L 193 " --> pdb=" O LEU L 210 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU L 210 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL L 195 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE L 208 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE L 197 " --> pdb=" O ILE L 206 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE L 206 " --> pdb=" O PHE L 197 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 223 through 224 removed outlier: 3.664A pdb=" N VAL L 223 " --> pdb=" O GLU L 231 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 43 through 50 removed outlier: 3.594A pdb=" N TYR M 45 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN M 49 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 149 through 151 removed outlier: 7.140A pdb=" N GLU M 79 " --> pdb=" O THR M 104 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA M 106 " --> pdb=" O MET M 77 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET M 77 " --> pdb=" O ALA M 106 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA M 188 " --> pdb=" O ILE M 215 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE M 215 " --> pdb=" O ALA M 188 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA M 190 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU M 213 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE M 192 " --> pdb=" O LYS M 211 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS M 211 " --> pdb=" O ILE M 192 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA M 209 " --> pdb=" O PRO M 194 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 196 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 213 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER M 163 " --> pdb=" O SER M 167 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 223 through 224 removed outlier: 3.640A pdb=" N VAL M 223 " --> pdb=" O GLU M 231 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 43 through 50 removed outlier: 3.893A pdb=" N TYR N 45 " --> pdb=" O LYS N 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS N 62 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN N 49 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 149 through 151 removed outlier: 5.659A pdb=" N ILE N 101 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS N 83 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL N 103 " --> pdb=" O GLU N 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU N 81 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LEU N 187 " --> pdb=" O ASP N 216 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP N 216 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS N 212 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR N 193 " --> pdb=" O LEU N 210 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU N 210 " --> pdb=" O THR N 193 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL N 195 " --> pdb=" O PHE N 208 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE N 208 " --> pdb=" O VAL N 195 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE N 197 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE N 206 " --> pdb=" O PHE N 197 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG N 199 " --> pdb=" O THR N 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR N 204 " --> pdb=" O ARG N 199 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER N 163 " --> pdb=" O SER N 167 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N SER N 167 " --> pdb=" O SER N 163 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 223 through 224 removed outlier: 3.698A pdb=" N VAL N 223 " --> pdb=" O GLU N 231 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 43 through 50 removed outlier: 3.689A pdb=" N ASN O 49 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 149 through 151 removed outlier: 7.163A pdb=" N GLU O 79 " --> pdb=" O THR O 104 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA O 106 " --> pdb=" O MET O 77 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET O 77 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA O 188 " --> pdb=" O ILE O 215 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE O 215 " --> pdb=" O ALA O 188 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA O 190 " --> pdb=" O LEU O 213 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU O 213 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE O 192 " --> pdb=" O LYS O 211 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS O 211 " --> pdb=" O ILE O 192 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA O 209 " --> pdb=" O PRO O 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL O 196 " --> pdb=" O THR O 207 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 223 through 224 removed outlier: 3.601A pdb=" N VAL O 223 " --> pdb=" O GLU O 231 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 43 through 50 removed outlier: 3.571A pdb=" N TYR P 45 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN P 49 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 149 through 151 removed outlier: 7.135A pdb=" N GLU P 79 " --> pdb=" O THR P 104 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA P 106 " --> pdb=" O MET P 77 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET P 77 " --> pdb=" O ALA P 106 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA P 188 " --> pdb=" O ILE P 215 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE P 215 " --> pdb=" O ALA P 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA P 190 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU P 213 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE P 192 " --> pdb=" O LYS P 211 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS P 211 " --> pdb=" O ILE P 192 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA P 209 " --> pdb=" O PRO P 194 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL P 196 " --> pdb=" O THR P 207 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU P 213 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER P 163 " --> pdb=" O SER P 167 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 223 through 224 removed outlier: 3.617A pdb=" N VAL P 223 " --> pdb=" O GLU P 231 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2673 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: 4.69 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8239 1.34 - 1.46: 4928 1.46 - 1.58: 12801 1.58 - 1.69: 0 1.69 - 1.81: 208 Bond restraints: 26176 Sorted by residual: bond pdb=" CA THR J 74 " pdb=" CB THR J 74 " ideal model delta sigma weight residual 1.525 1.543 -0.018 1.25e-02 6.40e+03 2.06e+00 bond pdb=" CA THR N 74 " pdb=" CB THR N 74 " ideal model delta sigma weight residual 1.525 1.540 -0.016 1.25e-02 6.40e+03 1.59e+00 bond pdb=" CB LEU J 226 " pdb=" CG LEU J 226 " ideal model delta sigma weight residual 1.530 1.552 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" N LEU J 226 " pdb=" CA LEU J 226 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 bond pdb=" CB GLN E 23 " pdb=" CG GLN E 23 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 ... (remaining 26171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 34471 1.77 - 3.55: 621 3.55 - 5.32: 108 5.32 - 7.09: 25 7.09 - 8.87: 7 Bond angle restraints: 35232 Sorted by residual: angle pdb=" CA GLU K 147 " pdb=" CB GLU K 147 " pdb=" CG GLU K 147 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.55e+01 angle pdb=" C GLY J 225 " pdb=" N LEU J 226 " pdb=" CA LEU J 226 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C ILE J 224 " pdb=" N GLY J 225 " pdb=" CA GLY J 225 " ideal model delta sigma weight residual 121.41 127.75 -6.34 1.96e+00 2.60e-01 1.05e+01 angle pdb=" CA GLN F 112 " pdb=" CB GLN F 112 " pdb=" CG GLN F 112 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.11e+00 angle pdb=" CA GLN A 112 " pdb=" CB GLN A 112 " pdb=" CG GLN A 112 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 ... (remaining 35227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13498 18.00 - 36.00: 1914 36.00 - 54.00: 589 54.00 - 72.00: 86 72.00 - 90.00: 105 Dihedral angle restraints: 16192 sinusoidal: 6368 harmonic: 9824 Sorted by residual: dihedral pdb=" CA GLY J 225 " pdb=" C GLY J 225 " pdb=" N LEU J 226 " pdb=" CA LEU J 226 " ideal model delta harmonic sigma weight residual -180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ALA J 221 " pdb=" C ALA J 221 " pdb=" N ASN J 222 " pdb=" CA ASN J 222 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET N 158 " pdb=" C MET N 158 " pdb=" N VAL N 159 " pdb=" CA VAL N 159 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 16189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3722 0.067 - 0.133: 509 0.133 - 0.200: 46 0.200 - 0.267: 10 0.267 - 0.333: 1 Chirality restraints: 4288 Sorted by residual: chirality pdb=" CB ILE J 224 " pdb=" CA ILE J 224 " pdb=" CG1 ILE J 224 " pdb=" CG2 ILE J 224 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR M 74 " pdb=" CA THR M 74 " pdb=" OG1 THR M 74 " pdb=" CG2 THR M 74 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB THR P 74 " pdb=" CA THR P 74 " pdb=" OG1 THR P 74 " pdb=" CG2 THR P 74 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4285 not shown) Planarity restraints: 4336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 45 " 0.008 2.00e-02 2.50e+03 1.01e-02 2.06e+00 pdb=" CG TYR I 45 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR I 45 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR I 45 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR I 45 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR I 45 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 45 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 111 " -0.010 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR A 111 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 111 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 111 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 111 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 31 " -0.007 2.00e-02 2.50e+03 9.45e-03 1.79e+00 pdb=" CG TYR M 31 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR M 31 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR M 31 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR M 31 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR M 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR M 31 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR M 31 " 0.002 2.00e-02 2.50e+03 ... (remaining 4333 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1999 2.74 - 3.28: 25349 3.28 - 3.82: 39410 3.82 - 4.36: 43335 4.36 - 4.90: 76390 Nonbonded interactions: 186483 Sorted by model distance: nonbonded pdb=" OH TYR N 118 " pdb=" OE2 GLU N 141 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG M 183 " pdb=" OE1 GLN M 186 " model vdw 2.205 3.120 nonbonded pdb=" O LYS B 145 " pdb=" OG SER B 148 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG F 183 " pdb=" OE1 GLN F 186 " model vdw 2.211 3.120 nonbonded pdb=" O LYS L 145 " pdb=" OG SER L 148 " model vdw 2.214 3.040 ... (remaining 186478 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26176 Z= 0.156 Angle : 0.629 8.866 35232 Z= 0.342 Chirality : 0.047 0.333 4288 Planarity : 0.003 0.043 4336 Dihedral : 19.562 90.004 9824 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 0.81 % Allowed : 34.76 % Favored : 64.43 % 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: -0.63 (0.14), residues: 3280 helix: 0.24 (0.19), residues: 703 sheet: 0.24 (0.17), residues: 818 loop : -1.00 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 171 TYR 0.025 0.002 TYR I 45 PHE 0.011 0.001 PHE C 98 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (26176) covalent geometry : angle 0.62950 / 0.34 (35232) hydrogen bonds : bond 0.18074 / 11.91 ( 1025) hydrogen bonds : angle 6.66092 / 4.58 ( 2673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 443 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.7965 (tppp) cc_final: 0.7250 (mtmm) REVERT: B 144 PHE cc_start: 0.7569 (m-10) cc_final: 0.7238 (m-10) REVERT: D 41 LYS cc_start: 0.7695 (tppp) cc_final: 0.7285 (mtmm) REVERT: H 75 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: I 37 LYS cc_start: 0.5627 (mttt) cc_final: 0.4883 (ttpt) REVERT: K 217 ARG cc_start: 0.6096 (tmm-80) cc_final: 0.5830 (tmt170) REVERT: L 132 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7588 (m-70) REVERT: N 144 PHE cc_start: 0.7546 (m-10) cc_final: 0.7204 (m-10) outliers start: 24 outliers final: 15 residues processed: 455 average time/residue: 0.1895 time to fit residues: 131.7557 Evaluate side-chains 414 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 397 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain O residue 112 GLN Chi-restraints excluded: chain P residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN F 112 GLN J 112 GLN J 123 HIS K 112 GLN L 112 GLN N 123 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163365 restraints weight = 44553.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167133 restraints weight = 29403.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169711 restraints weight = 22201.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.171490 restraints weight = 18263.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172781 restraints weight = 15900.940| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26176 Z= 0.161 Angle : 0.588 8.568 35232 Z= 0.316 Chirality : 0.047 0.222 4288 Planarity : 0.003 0.034 4336 Dihedral : 5.041 49.775 3600 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.51 % Allowed : 31.62 % Favored : 62.87 % 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: -0.50 (0.14), residues: 3280 helix: 0.51 (0.19), residues: 719 sheet: 0.23 (0.17), residues: 822 loop : -0.96 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 217 TYR 0.018 0.002 TYR B 111 PHE 0.008 0.001 PHE O 98 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (26176) covalent geometry : angle 0.58832 / 0.32 (35232) hydrogen bonds : bond 0.04399 / 2.97 ( 1025) hydrogen bonds : angle 5.20663 / 3.57 ( 2673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 456 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.7976 (tppp) cc_final: 0.7141 (mtmm) REVERT: C 45 TYR cc_start: 0.6941 (p90) cc_final: 0.6682 (p90) REVERT: D 184 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: E 126 ARG cc_start: 0.4972 (ptt180) cc_final: 0.4453 (ptm160) REVERT: G 45 TYR cc_start: 0.6913 (p90) cc_final: 0.6441 (p90) REVERT: H 75 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: H 81 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6398 (mm-30) REVERT: I 231 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: L 132 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7728 (m-70) REVERT: L 144 PHE cc_start: 0.7559 (m-80) cc_final: 0.7298 (m-10) REVERT: N 210 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8226 (tp) outliers start: 163 outliers final: 110 residues processed: 581 average time/residue: 0.1652 time to fit residues: 151.8792 Evaluate side-chains 504 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 389 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 211 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN E 112 GLN F 112 GLN H 112 GLN J 112 GLN K 112 GLN L 112 GLN M 112 GLN N 112 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159315 restraints weight = 44466.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163104 restraints weight = 28578.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165706 restraints weight = 21343.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167492 restraints weight = 17439.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168771 restraints weight = 15143.547| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26176 Z= 0.254 Angle : 0.685 9.014 35232 Z= 0.371 Chirality : 0.048 0.213 4288 Planarity : 0.004 0.044 4336 Dihedral : 5.393 39.926 3586 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 8.78 % Allowed : 30.03 % Favored : 61.18 % 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 (0.14), residues: 3280 helix: 0.02 (0.19), residues: 719 sheet: -0.21 (0.18), residues: 807 loop : -1.14 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 217 TYR 0.021 0.003 TYR M 111 PHE 0.010 0.002 PHE A 98 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 (26176) covalent geometry : angle 0.68530 / 0.37 (35232) hydrogen bonds : bond 0.05299 / 3.56 ( 1025) hydrogen bonds : angle 5.59106 / 3.84 ( 2673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 448 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5752 (p0) REVERT: B 75 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: B 210 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8212 (tp) REVERT: C 45 TYR cc_start: 0.6719 (p90) cc_final: 0.6390 (p90) REVERT: D 210 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8227 (tp) REVERT: E 231 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: F 210 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8142 (tp) REVERT: G 45 TYR cc_start: 0.6692 (p90) cc_final: 0.6318 (p90) REVERT: G 87 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6366 (p0) REVERT: G 210 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (tp) REVERT: H 75 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: H 81 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6521 (mm-30) REVERT: H 210 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8130 (tp) REVERT: I 231 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: K 87 ASN cc_start: 0.6136 (OUTLIER) cc_final: 0.5912 (p0) REVERT: L 144 PHE cc_start: 0.7707 (m-80) cc_final: 0.7413 (m-10) REVERT: L 210 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8245 (tp) REVERT: M 126 ARG cc_start: 0.5211 (ptt180) cc_final: 0.5002 (ptm160) REVERT: N 45 TYR cc_start: 0.6875 (p90) cc_final: 0.6371 (p90) REVERT: N 210 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8244 (tp) REVERT: O 231 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: P 75 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: P 132 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7855 (m170) REVERT: P 210 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8144 (tp) REVERT: P 217 ARG cc_start: 0.6345 (tmm-80) cc_final: 0.5915 (ttp-170) outliers start: 260 outliers final: 175 residues processed: 656 average time/residue: 0.1592 time to fit residues: 167.9844 Evaluate side-chains 587 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 394 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 87 ASN Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 162 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 111 TYR Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 219 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 231 GLU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 HIS Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 178 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 247 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 242 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN F 112 GLN H 112 GLN J 112 GLN J 123 HIS K 112 GLN L 112 GLN N 112 GLN N 123 HIS O 112 GLN P 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.194344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165576 restraints weight = 43668.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169543 restraints weight = 27894.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172288 restraints weight = 20706.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.174220 restraints weight = 16847.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.175576 restraints weight = 14506.771| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26176 Z= 0.107 Angle : 0.555 8.421 35232 Z= 0.296 Chirality : 0.046 0.241 4288 Planarity : 0.003 0.034 4336 Dihedral : 4.590 35.710 3582 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.88 % Allowed : 32.97 % Favored : 61.15 % 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: -0.46 (0.15), residues: 3280 helix: 0.58 (0.20), residues: 734 sheet: 0.04 (0.17), residues: 882 loop : -0.85 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 171 TYR 0.022 0.002 TYR E 111 PHE 0.008 0.001 PHE O 98 HIS 0.001 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (26176) covalent geometry : angle 0.55530 / 0.30 (35232) hydrogen bonds : bond 0.03597 / 2.41 ( 1025) hydrogen bonds : angle 4.70679 / 3.24 ( 2673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 492 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.7977 (tppp) cc_final: 0.7300 (mtmm) REVERT: C 45 TYR cc_start: 0.6975 (p90) cc_final: 0.6752 (p90) REVERT: D 75 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: D 184 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: E 126 ARG cc_start: 0.5405 (ptt180) cc_final: 0.5147 (ptm160) REVERT: E 217 ARG cc_start: 0.6149 (tmm-80) cc_final: 0.5871 (ttt-90) REVERT: E 231 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: F 75 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: F 109 MET cc_start: 0.8218 (ttm) cc_final: 0.7905 (ttm) REVERT: G 45 TYR cc_start: 0.6801 (p90) cc_final: 0.6534 (p90) REVERT: G 227 SER cc_start: 0.8039 (m) cc_final: 0.7762 (p) REVERT: H 81 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6443 (mm-30) REVERT: I 70 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6531 (mp10) REVERT: I 217 ARG cc_start: 0.6298 (tmm-80) cc_final: 0.6057 (ttt-90) REVERT: L 41 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6832 (ttmm) REVERT: L 132 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7754 (m-70) REVERT: L 144 PHE cc_start: 0.7645 (m-80) cc_final: 0.7342 (m-10) REVERT: M 31 TYR cc_start: 0.5993 (t80) cc_final: 0.5667 (t80) REVERT: M 81 GLU cc_start: 0.7000 (tp30) cc_final: 0.6771 (tp30) REVERT: O 126 ARG cc_start: 0.5619 (ptt180) cc_final: 0.5290 (ptm160) REVERT: P 75 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7241 (m-10) outliers start: 174 outliers final: 121 residues processed: 618 average time/residue: 0.1707 time to fit residues: 166.1568 Evaluate side-chains 540 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 411 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 237 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 288 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN C 112 GLN D 112 GLN E 112 GLN F 112 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN K 112 GLN L 112 GLN N 112 GLN N 123 HIS O 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.190244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161199 restraints weight = 43882.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165236 restraints weight = 27376.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167998 restraints weight = 20149.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169908 restraints weight = 16317.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.171243 restraints weight = 14082.588| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26176 Z= 0.182 Angle : 0.613 8.237 35232 Z= 0.330 Chirality : 0.047 0.229 4288 Planarity : 0.003 0.040 4336 Dihedral : 4.876 36.651 3580 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 8.28 % Allowed : 31.59 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.77 (0.14), residues: 3280 helix: 0.20 (0.19), residues: 734 sheet: -0.11 (0.18), residues: 807 loop : -0.99 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 171 TYR 0.018 0.002 TYR P 111 PHE 0.008 0.001 PHE B 75 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (26176) covalent geometry : angle 0.61341 / 0.33 (35232) hydrogen bonds : bond 0.04432 / 2.97 ( 1025) hydrogen bonds : angle 5.02283 / 3.45 ( 2673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 451 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.6347 (OUTLIER) cc_final: 0.6120 (p0) REVERT: A 218 GLU cc_start: 0.7774 (pt0) cc_final: 0.7135 (pm20) REVERT: B 41 LYS cc_start: 0.8045 (tppp) cc_final: 0.7315 (mtmm) REVERT: C 45 TYR cc_start: 0.6935 (p90) cc_final: 0.6666 (p90) REVERT: C 210 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 184 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: D 235 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7133 (tmm) REVERT: E 126 ARG cc_start: 0.5593 (ptt180) cc_final: 0.5251 (ptm160) REVERT: E 217 ARG cc_start: 0.6188 (tmm-80) cc_final: 0.5767 (tmm160) REVERT: E 231 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: F 75 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: F 210 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8122 (tp) REVERT: G 45 TYR cc_start: 0.6711 (p90) cc_final: 0.6425 (p90) REVERT: G 227 SER cc_start: 0.8021 (m) cc_final: 0.7786 (p) REVERT: G 231 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: H 81 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6362 (mm-30) REVERT: I 45 TYR cc_start: 0.7057 (p90) cc_final: 0.6461 (p90) REVERT: I 70 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6689 (mp10) REVERT: I 126 ARG cc_start: 0.5466 (ptt180) cc_final: 0.5187 (ptm160) REVERT: J 210 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8121 (tp) REVERT: L 41 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.6994 (ttmm) REVERT: L 132 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7748 (m-70) REVERT: L 210 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8228 (tp) REVERT: M 210 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8149 (tp) REVERT: N 210 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8203 (tp) REVERT: O 231 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: P 75 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: P 210 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8115 (tp) REVERT: P 227 SER cc_start: 0.8076 (m) cc_final: 0.7831 (p) outliers start: 245 outliers final: 164 residues processed: 647 average time/residue: 0.1640 time to fit residues: 168.9372 Evaluate side-chains 597 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 415 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 132 HIS Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 162 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 219 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 231 GLU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 229 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 139 optimal weight: 0.0770 chunk 80 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN C 112 GLN D 112 GLN F 112 GLN J 112 GLN J 123 HIS K 112 GLN L 112 GLN N 112 GLN N 123 HIS O 112 GLN P 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.192681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163406 restraints weight = 44280.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167318 restraints weight = 28922.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170127 restraints weight = 21683.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.172164 restraints weight = 17614.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173596 restraints weight = 15116.246| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26176 Z= 0.107 Angle : 0.551 7.687 35232 Z= 0.293 Chirality : 0.046 0.245 4288 Planarity : 0.003 0.034 4336 Dihedral : 4.444 33.943 3580 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.42 % Allowed : 33.14 % Favored : 60.44 % 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: -0.45 (0.15), residues: 3280 helix: 0.55 (0.20), residues: 734 sheet: 0.07 (0.18), residues: 882 loop : -0.85 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 171 TYR 0.020 0.002 TYR M 31 PHE 0.007 0.001 PHE O 98 HIS 0.002 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (26176) covalent geometry : angle 0.55064 / 0.29 (35232) hydrogen bonds : bond 0.03495 / 2.34 ( 1025) hydrogen bonds : angle 4.57976 / 3.14 ( 2673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 487 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7431 (ttpp) cc_final: 0.6963 (tttp) REVERT: A 218 GLU cc_start: 0.7704 (pt0) cc_final: 0.7034 (pm20) REVERT: B 41 LYS cc_start: 0.7969 (tppp) cc_final: 0.7264 (mtmm) REVERT: B 210 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 45 TYR cc_start: 0.7048 (p90) cc_final: 0.6807 (p90) REVERT: D 75 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: D 184 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: D 235 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7127 (tmm) REVERT: E 126 ARG cc_start: 0.5451 (ptt180) cc_final: 0.5187 (ptm160) REVERT: F 75 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: G 45 TYR cc_start: 0.6918 (p90) cc_final: 0.6655 (p90) REVERT: G 81 GLU cc_start: 0.6899 (tp30) cc_final: 0.6636 (tp30) REVERT: G 227 SER cc_start: 0.7952 (m) cc_final: 0.7704 (p) REVERT: H 81 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6412 (mm-30) REVERT: H 210 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8000 (tp) REVERT: I 45 TYR cc_start: 0.7098 (p90) cc_final: 0.6493 (p90) REVERT: I 70 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: I 231 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: J 210 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (tp) REVERT: L 31 TYR cc_start: 0.5692 (t80) cc_final: 0.5340 (t80) REVERT: L 75 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: M 33 LYS cc_start: 0.7457 (ttpp) cc_final: 0.7000 (tttp) REVERT: M 81 GLU cc_start: 0.7054 (tp30) cc_final: 0.6826 (tp30) REVERT: N 45 TYR cc_start: 0.7198 (p90) cc_final: 0.6907 (p90) REVERT: O 109 MET cc_start: 0.8023 (ttt) cc_final: 0.7401 (ttm) REVERT: O 126 ARG cc_start: 0.5715 (ptt180) cc_final: 0.5509 (ptm160) REVERT: O 217 ARG cc_start: 0.6909 (tmt170) cc_final: 0.6451 (ptt90) REVERT: P 75 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: P 227 SER cc_start: 0.8049 (m) cc_final: 0.7838 (p) outliers start: 190 outliers final: 148 residues processed: 633 average time/residue: 0.1669 time to fit residues: 166.6572 Evaluate side-chains 587 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 428 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 220 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN C 112 GLN D 112 GLN E 112 GLN F 112 GLN G 112 GLN H 112 GLN J 112 GLN K 112 GLN L 112 GLN M 112 GLN N 112 GLN N 123 HIS O 112 GLN P 112 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.188921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.160063 restraints weight = 44278.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163855 restraints weight = 29235.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166520 restraints weight = 22033.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168423 restraints weight = 18034.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169812 restraints weight = 15579.471| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26176 Z= 0.161 Angle : 0.591 8.434 35232 Z= 0.318 Chirality : 0.046 0.220 4288 Planarity : 0.003 0.041 4336 Dihedral : 4.630 33.136 3576 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 8.38 % Allowed : 31.52 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.14), residues: 3280 helix: 0.26 (0.19), residues: 734 sheet: -0.04 (0.19), residues: 807 loop : -0.96 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 171 TYR 0.018 0.002 TYR M 45 PHE 0.011 0.001 PHE B 75 HIS 0.004 0.001 HIS L 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (26176) covalent geometry : angle 0.59116 / 0.32 (35232) hydrogen bonds : bond 0.04172 / 2.80 ( 1025) hydrogen bonds : angle 4.87190 / 3.34 ( 2673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 453 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8195 (tp) REVERT: A 218 GLU cc_start: 0.7745 (pt0) cc_final: 0.7125 (pm20) REVERT: B 41 LYS cc_start: 0.8014 (tppp) cc_final: 0.7286 (mtmm) REVERT: B 210 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8174 (tp) REVERT: C 45 TYR cc_start: 0.7037 (p90) cc_final: 0.6777 (p90) REVERT: C 210 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8059 (tp) REVERT: D 45 TYR cc_start: 0.6865 (p90) cc_final: 0.6645 (p90) REVERT: D 75 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: D 184 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: D 210 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8175 (tp) REVERT: D 235 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7153 (tmm) REVERT: E 126 ARG cc_start: 0.5562 (ptt180) cc_final: 0.5348 (ptm160) REVERT: E 231 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: F 75 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: G 45 TYR cc_start: 0.6881 (p90) cc_final: 0.6607 (p90) REVERT: H 75 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: H 210 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8067 (tp) REVERT: I 45 TYR cc_start: 0.7016 (p90) cc_final: 0.6540 (p90) REVERT: I 70 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6597 (mp10) REVERT: I 231 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: J 210 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8153 (tp) REVERT: L 41 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7092 (ttmm) REVERT: L 75 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: L 81 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6575 (mm-30) REVERT: L 210 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8215 (tp) REVERT: M 210 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (tp) REVERT: M 231 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: N 45 TYR cc_start: 0.7244 (p90) cc_final: 0.6935 (p90) REVERT: O 109 MET cc_start: 0.8029 (ttt) cc_final: 0.7491 (ttm) REVERT: O 217 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6486 (ptt90) REVERT: P 75 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: P 227 SER cc_start: 0.8124 (m) cc_final: 0.7921 (p) outliers start: 248 outliers final: 182 residues processed: 641 average time/residue: 0.1642 time to fit residues: 168.1803 Evaluate side-chains 623 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 421 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 219 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 212 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 50 optimal weight: 0.0060 chunk 158 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 132 HIS B 112 GLN C 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN J 112 GLN K 112 GLN L 112 GLN N 112 GLN N 123 HIS O 112 GLN P 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.193570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.164189 restraints weight = 44016.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168114 restraints weight = 28881.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170903 restraints weight = 21658.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172947 restraints weight = 17644.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174392 restraints weight = 15137.801| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26176 Z= 0.103 Angle : 0.552 8.668 35232 Z= 0.292 Chirality : 0.046 0.254 4288 Planarity : 0.003 0.034 4336 Dihedral : 4.208 29.300 3574 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 6.39 % Allowed : 33.28 % Favored : 60.34 % 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: -0.42 (0.15), residues: 3280 helix: 0.54 (0.19), residues: 734 sheet: 0.09 (0.18), residues: 882 loop : -0.81 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 171 TYR 0.022 0.001 TYR E 111 PHE 0.008 0.001 PHE B 75 HIS 0.002 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (26176) covalent geometry : angle 0.55197 / 0.29 (35232) hydrogen bonds : bond 0.03352 / 2.24 ( 1025) hydrogen bonds : angle 4.51581 / 3.11 ( 2673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 470 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7400 (ttpp) cc_final: 0.6933 (tttp) REVERT: A 109 MET cc_start: 0.8037 (ttt) cc_final: 0.7481 (ttm) REVERT: A 218 GLU cc_start: 0.7715 (pt0) cc_final: 0.7014 (pm20) REVERT: B 41 LYS cc_start: 0.7943 (tppp) cc_final: 0.7252 (mtmm) REVERT: C 45 TYR cc_start: 0.7131 (p90) cc_final: 0.6873 (p90) REVERT: C 75 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: D 41 LYS cc_start: 0.7991 (tppp) cc_final: 0.7145 (mtmm) REVERT: D 75 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: D 184 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: D 235 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7155 (tmm) REVERT: G 45 TYR cc_start: 0.6923 (p90) cc_final: 0.6708 (p90) REVERT: G 81 GLU cc_start: 0.6940 (tp30) cc_final: 0.6699 (tp30) REVERT: H 210 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (tp) REVERT: I 45 TYR cc_start: 0.7184 (p90) cc_final: 0.6911 (p90) REVERT: I 70 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6479 (mp10) REVERT: J 210 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (tp) REVERT: L 41 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7047 (ttmm) REVERT: L 75 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: L 81 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6533 (mm-30) REVERT: L 210 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (tp) REVERT: M 33 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7120 (tttp) REVERT: M 81 GLU cc_start: 0.6993 (tp30) cc_final: 0.6782 (tp30) REVERT: M 218 GLU cc_start: 0.7563 (pt0) cc_final: 0.6903 (pm20) REVERT: N 45 TYR cc_start: 0.7308 (p90) cc_final: 0.7058 (p90) REVERT: O 109 MET cc_start: 0.7967 (ttt) cc_final: 0.7430 (ttm) REVERT: O 217 ARG cc_start: 0.6912 (tmt170) cc_final: 0.6566 (ttp80) REVERT: O 231 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: P 75 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7229 (m-10) outliers start: 189 outliers final: 153 residues processed: 618 average time/residue: 0.1536 time to fit residues: 151.0770 Evaluate side-chains 595 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 430 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 132 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 42 CYS Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 162 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 231 GLU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 230 optimal weight: 0.0980 chunk 171 optimal weight: 0.9990 chunk 304 optimal weight: 0.0970 chunk 23 optimal weight: 0.0870 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN C 112 GLN D 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 112 GLN G 186 GLN H 112 GLN I 112 GLN K 112 GLN L 112 GLN N 112 GLN N 123 HIS ** O 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.195273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166231 restraints weight = 44073.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170055 restraints weight = 29449.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.172738 restraints weight = 22291.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174669 restraints weight = 18250.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.176089 restraints weight = 15791.741| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26176 Z= 0.099 Angle : 0.542 8.418 35232 Z= 0.287 Chirality : 0.046 0.234 4288 Planarity : 0.003 0.034 4336 Dihedral : 4.014 28.919 3574 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 6.32 % Allowed : 33.58 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.33 (0.15), residues: 3280 helix: 0.50 (0.19), residues: 734 sheet: 0.19 (0.18), residues: 878 loop : -0.72 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 171 TYR 0.016 0.001 TYR N 111 PHE 0.011 0.001 PHE F 75 HIS 0.002 0.000 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (26176) covalent geometry : angle 0.54168 / 0.29 (35232) hydrogen bonds : bond 0.03187 / 2.15 ( 1025) hydrogen bonds : angle 4.37455 / 3.01 ( 2673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 463 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7900 (ttt) cc_final: 0.7335 (ttm) REVERT: A 196 VAL cc_start: 0.8382 (t) cc_final: 0.8157 (t) REVERT: A 218 GLU cc_start: 0.7697 (pt0) cc_final: 0.7017 (pm20) REVERT: B 41 LYS cc_start: 0.7966 (tppp) cc_final: 0.7277 (mtmm) REVERT: B 227 SER cc_start: 0.8333 (m) cc_final: 0.7729 (t) REVERT: C 45 TYR cc_start: 0.7088 (p90) cc_final: 0.6839 (p90) REVERT: C 75 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: D 41 LYS cc_start: 0.7894 (tppp) cc_final: 0.7060 (mtmm) REVERT: D 235 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7154 (tmm) REVERT: E 171 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6744 (tpp80) REVERT: E 231 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: F 109 MET cc_start: 0.7891 (ttm) cc_final: 0.7428 (ttm) REVERT: G 45 TYR cc_start: 0.7122 (p90) cc_final: 0.6888 (p90) REVERT: G 109 MET cc_start: 0.8249 (ttt) cc_final: 0.7720 (ttm) REVERT: G 171 ARG cc_start: 0.7251 (tpp80) cc_final: 0.6938 (mmm-85) REVERT: H 77 MET cc_start: 0.6968 (ttt) cc_final: 0.6614 (ttp) REVERT: H 210 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (tp) REVERT: H 227 SER cc_start: 0.8471 (m) cc_final: 0.8144 (p) REVERT: I 45 TYR cc_start: 0.7175 (p90) cc_final: 0.6910 (p90) REVERT: I 70 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6323 (mp10) REVERT: J 210 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (tp) REVERT: L 41 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7255 (mtmm) REVERT: L 75 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: L 81 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6577 (mm-30) REVERT: L 210 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8163 (tp) REVERT: M 33 LYS cc_start: 0.7384 (ttpp) cc_final: 0.7131 (tttp) REVERT: M 218 GLU cc_start: 0.7599 (pt0) cc_final: 0.6946 (pm20) REVERT: N 45 TYR cc_start: 0.7259 (p90) cc_final: 0.7026 (p90) REVERT: O 109 MET cc_start: 0.7843 (ttt) cc_final: 0.7311 (ttm) REVERT: O 217 ARG cc_start: 0.6962 (tmt170) cc_final: 0.6654 (ttp80) outliers start: 187 outliers final: 157 residues processed: 611 average time/residue: 0.1529 time to fit residues: 148.5407 Evaluate side-chains 599 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 433 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 237 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN C 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 112 GLN I 112 GLN J 112 GLN ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN M 112 GLN N 112 GLN ** O 112 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 = 0.4305 r_free = 0.4305 target = 0.189863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.160148 restraints weight = 44589.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164006 restraints weight = 29391.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166713 restraints weight = 22166.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.168681 restraints weight = 18167.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170089 restraints weight = 15705.521| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26176 Z= 0.164 Angle : 0.607 8.168 35232 Z= 0.325 Chirality : 0.046 0.241 4288 Planarity : 0.003 0.038 4336 Dihedral : 4.474 33.487 3574 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.59 % Allowed : 33.45 % Favored : 59.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.15), residues: 3280 helix: 0.22 (0.19), residues: 734 sheet: 0.09 (0.19), residues: 803 loop : -0.85 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 171 TYR 0.022 0.002 TYR K 111 PHE 0.010 0.001 PHE D 75 HIS 0.003 0.001 HIS L 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (26176) covalent geometry : angle 0.60651 / 0.32 (35232) hydrogen bonds : bond 0.04138 / 2.78 ( 1025) hydrogen bonds : angle 4.84551 / 3.32 ( 2673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 447 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7930 (ttt) cc_final: 0.7365 (ttm) REVERT: A 218 GLU cc_start: 0.7744 (pt0) cc_final: 0.7108 (pm20) REVERT: B 41 LYS cc_start: 0.7991 (tppp) cc_final: 0.7264 (mtmm) REVERT: B 210 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8189 (tp) REVERT: C 45 TYR cc_start: 0.7044 (p90) cc_final: 0.6757 (p90) REVERT: C 75 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7125 (m-10) REVERT: C 210 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8045 (tp) REVERT: D 41 LYS cc_start: 0.7947 (tppp) cc_final: 0.7016 (mtmm) REVERT: D 45 TYR cc_start: 0.6937 (p90) cc_final: 0.6675 (p90) REVERT: D 184 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: D 235 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7313 (tmm) REVERT: E 231 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: F 109 MET cc_start: 0.7779 (ttm) cc_final: 0.7500 (ttm) REVERT: G 45 TYR cc_start: 0.7088 (p90) cc_final: 0.6791 (p90) REVERT: H 210 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8104 (tp) REVERT: I 45 TYR cc_start: 0.7076 (p90) cc_final: 0.6764 (p90) REVERT: I 70 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: I 231 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: J 210 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8195 (tp) REVERT: L 41 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7398 (mtmm) REVERT: L 75 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: L 210 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8262 (tp) REVERT: M 33 LYS cc_start: 0.7557 (ttpp) cc_final: 0.7081 (tttp) REVERT: M 218 GLU cc_start: 0.7637 (pt0) cc_final: 0.7027 (pm20) REVERT: N 45 TYR cc_start: 0.7175 (p90) cc_final: 0.6893 (p90) REVERT: N 77 MET cc_start: 0.7309 (ttt) cc_final: 0.6959 (ttp) REVERT: N 210 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8197 (tp) REVERT: O 109 MET cc_start: 0.7835 (ttt) cc_final: 0.7260 (ttm) REVERT: O 217 ARG cc_start: 0.6928 (tmt170) cc_final: 0.6612 (ttp80) REVERT: O 231 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7324 (mt-10) outliers start: 195 outliers final: 159 residues processed: 596 average time/residue: 0.1659 time to fit residues: 157.6740 Evaluate side-chains 612 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 438 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 112 GLN Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 125 GLU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 219 VAL Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 231 GLU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 315 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 249 optimal weight: 0.0000 chunk 55 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS O 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.190126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160424 restraints weight = 44184.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164282 restraints weight = 29129.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167023 restraints weight = 21942.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169030 restraints weight = 17951.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.170376 restraints weight = 15466.937| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.328 26176 Z= 0.299 Angle : 1.041 59.195 35232 Z= 0.628 Chirality : 0.050 1.094 4288 Planarity : 0.005 0.202 4336 Dihedral : 4.476 33.409 3574 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.49 % Allowed : 33.61 % Favored : 59.90 % Cbeta Deviations : 0.16 % 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: -0.62 (0.15), residues: 3280 helix: 0.16 (0.19), residues: 734 sheet: 0.09 (0.19), residues: 803 loop : -0.86 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 126 TYR 0.026 0.002 TYR M 111 PHE 0.009 0.001 PHE K 98 HIS 0.003 0.001 HIS L 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.30 (26176) covalent geometry : angle 1.04081 / 0.63 (35232) hydrogen bonds : bond 0.04235 / 2.86 ( 1025) hydrogen bonds : angle 4.84901 / 3.33 ( 2673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.50 seconds wall clock time: 80 minutes 32.11 seconds (4832.11 seconds total)