Starting phenix.real_space_refine on Mon Apr 6 09:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d08_30526/04_2026/7d08_30526.map" } resolution = 4.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 88 5.16 5 C 11342 2.51 5 N 2988 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "E" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.29, per 1000 atoms: 0.24 Number of scatterers: 17802 At special positions: 0 Unit cell: (130.44, 123.918, 150.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 6 15.00 O 3378 8.00 N 2988 7.00 C 11342 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: 1.58 Conformation dependent library (CDL) restraints added in 731.7 milliseconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 17 sheets defined 45.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 30 removed outlier: 3.831A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.829A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 79 removed outlier: 3.611A pdb=" N ILE A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.855A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.530A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.507A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.767A pdb=" N GLN A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 3.627A pdb=" N ARG A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 removed outlier: 3.740A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 4.089A pdb=" N TRP A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.628A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 removed outlier: 4.322A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.027A pdb=" N ARG B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.657A pdb=" N PHE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.684A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 137 removed outlier: 4.080A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.978A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 200 removed outlier: 4.062A pdb=" N ARG B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 234 through 239 removed outlier: 4.122A pdb=" N GLN B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 239' Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 50 through 64 removed outlier: 3.613A pdb=" N VAL C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 removed outlier: 3.610A pdb=" N ILE C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 30 removed outlier: 3.830A pdb=" N ALA D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.830A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 79 removed outlier: 3.611A pdb=" N ILE D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.855A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.531A pdb=" N ALA D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.506A pdb=" N GLU D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.766A pdb=" N GLN D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 150 removed outlier: 3.628A pdb=" N ARG D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 173 removed outlier: 3.739A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 197 through 220 removed outlier: 3.629A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 254 removed outlier: 4.322A pdb=" N VAL D 236 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 242 " --> pdb=" O TYR D 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 61 removed outlier: 4.026A pdb=" N ARG E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.658A pdb=" N PHE E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 87 " --> pdb=" O GLN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 117 removed outlier: 3.683A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 122 through 137 removed outlier: 4.080A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.977A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 200 removed outlier: 4.063A pdb=" N ARG E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.121A pdb=" N GLN E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 239' Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.613A pdb=" N VAL F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 64 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 86 removed outlier: 3.611A pdb=" N ILE F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 10 removed outlier: 3.873A pdb=" N ALA G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 26 removed outlier: 3.669A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 110 removed outlier: 3.601A pdb=" N VAL G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 108 " --> pdb=" O ASN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 123 removed outlier: 4.112A pdb=" N GLN G 122 " --> pdb=" O THR G 119 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN G 123 " --> pdb=" O PRO G 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 119 through 123' Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.583A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER G 132 " --> pdb=" O GLN G 128 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.989A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 28 removed outlier: 3.771A pdb=" N LEU H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 102 removed outlier: 3.696A pdb=" N GLU H 100 " --> pdb=" O GLU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 126 through 135 removed outlier: 3.789A pdb=" N ILE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 3.645A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 26 removed outlier: 3.611A pdb=" N LEU I 8 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 110 removed outlier: 3.658A pdb=" N VAL I 101 " --> pdb=" O GLN I 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 135 removed outlier: 3.628A pdb=" N GLN I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN I 129 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN I 133 " --> pdb=" O GLN I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 193 removed outlier: 3.702A pdb=" N LEU I 188 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 26 removed outlier: 3.624A pdb=" N LEU J 8 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 3.645A pdb=" N GLU J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 134 removed outlier: 3.744A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 193 removed outlier: 3.849A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE J 193 " --> pdb=" O ILE J 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 30 removed outlier: 4.003A pdb=" N ILE K 12 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 101 through 106 Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.864A pdb=" N GLN K 117 " --> pdb=" O ASP K 114 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA K 118 " --> pdb=" O TYR K 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 114 through 118' Processing helix chain 'K' and resid 123 through 131 removed outlier: 3.736A pdb=" N GLU K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN K 129 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.970A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 29 removed outlier: 3.678A pdb=" N GLY L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 101 removed outlier: 3.827A pdb=" N GLU L 100 " --> pdb=" O GLN L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'L' and resid 122 through 132 removed outlier: 3.629A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 192 removed outlier: 3.708A pdb=" N LEU L 188 " --> pdb=" O ASP L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.410A pdb=" N LEU B 34 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU B 15 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.234A pdb=" N ALA B 43 " --> pdb=" O TYR B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.513A pdb=" N MET B 172 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 13 removed outlier: 5.717A pdb=" N LEU C 9 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 11 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 46 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY C 13 " --> pdb=" O LEU C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.410A pdb=" N LEU E 34 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU E 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.233A pdb=" N ALA E 43 " --> pdb=" O TYR E 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 92 through 95 removed outlier: 3.545A pdb=" N MET E 172 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 204 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 9 through 13 removed outlier: 5.717A pdb=" N LEU F 9 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS F 44 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL F 11 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 46 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY F 13 " --> pdb=" O LEU F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 44 removed outlier: 6.947A pdb=" N LEU G 79 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU G 73 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR G 81 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE G 71 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR G 83 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE G 146 " --> pdb=" O GLN G 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 175 through 176 removed outlier: 9.380A pdb=" N ILE H 176 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS H 43 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 83 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER H 70 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP H 85 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL H 68 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 59 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL H 148 " --> pdb=" O GLN H 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 146 through 149 removed outlier: 3.577A pdb=" N TYR I 158 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE I 161 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR I 83 " --> pdb=" O ASP I 69 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE I 71 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR I 81 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU I 73 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU I 79 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N ILE I 176 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS I 43 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 137 through 138 removed outlier: 3.949A pdb=" N LEU I 170 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 40 through 46 removed outlier: 3.807A pdb=" N PHE J 84 " --> pdb=" O MET J 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.745A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 157 through 162 removed outlier: 3.517A pdb=" N ALA J 149 " --> pdb=" O TYR J 158 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL J 148 " --> pdb=" O GLN J 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 146 through 148 removed outlier: 6.545A pdb=" N LYS K 57 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE K 161 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY K 66 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP K 87 " --> pdb=" O GLY K 66 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL K 68 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP K 85 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N ILE K 176 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS K 43 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 41 through 45 removed outlier: 5.635A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE L 161 " --> pdb=" O THR L 59 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1899 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: 2.63 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4966 1.33 - 1.45: 2693 1.45 - 1.57: 10205 1.57 - 1.69: 12 1.69 - 1.81: 168 Bond restraints: 18044 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.55e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.00e+01 bond pdb=" C5 ATP B 301 " pdb=" N7 ATP B 301 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.11e+01 ... (remaining 18039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 23779 3.17 - 6.35: 564 6.35 - 9.52: 93 9.52 - 12.70: 10 12.70 - 15.87: 4 Bond angle restraints: 24450 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 124.00 15.87 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 124.01 15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 122.02 14.81 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 122.07 14.76 1.00e+00 1.00e+00 2.18e+02 angle pdb=" N SER K 29 " pdb=" CA SER K 29 " pdb=" C SER K 29 " ideal model delta sigma weight residual 111.03 98.44 12.59 1.11e+00 8.12e-01 1.29e+02 ... (remaining 24445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9435 17.85 - 35.70: 977 35.70 - 53.55: 306 53.55 - 71.40: 126 71.40 - 89.25: 30 Dihedral angle restraints: 10874 sinusoidal: 4132 harmonic: 6742 Sorted by residual: dihedral pdb=" CA PRO D 225 " pdb=" C PRO D 225 " pdb=" N GLU D 226 " pdb=" CA GLU D 226 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO A 225 " pdb=" C PRO A 225 " pdb=" N GLU A 226 " pdb=" CA GLU A 226 " ideal model delta harmonic sigma weight residual 180.00 150.14 29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TYR G 169 " pdb=" C TYR G 169 " pdb=" N LEU G 170 " pdb=" CA LEU G 170 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 10871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2317 0.066 - 0.132: 542 0.132 - 0.199: 79 0.199 - 0.265: 22 0.265 - 0.331: 6 Chirality restraints: 2966 Sorted by residual: chirality pdb=" CA ASP D 135 " pdb=" N ASP D 135 " pdb=" C ASP D 135 " pdb=" CB ASP D 135 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ASP A 135 " pdb=" N ASP A 135 " pdb=" C ASP A 135 " pdb=" CB ASP A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ILE B 204 " pdb=" N ILE B 204 " pdb=" C ILE B 204 " pdb=" CB ILE B 204 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2963 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 64 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 65 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 64 " 0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO F 65 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 65 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 65 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 27 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C VAL E 27 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL E 27 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE E 28 " 0.018 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 289 2.57 - 3.15: 14695 3.15 - 3.73: 27257 3.73 - 4.32: 36677 4.32 - 4.90: 59079 Nonbonded interactions: 137997 Sorted by model distance: nonbonded pdb=" N GLU B 25 " pdb=" OE1 GLU B 25 " model vdw 1.987 3.120 nonbonded pdb=" N GLU E 25 " pdb=" OE1 GLU E 25 " model vdw 2.127 3.120 nonbonded pdb=" OD1 ASP B 268 " pdb=" N ASN B 269 " model vdw 2.165 3.120 nonbonded pdb=" CG2 VAL D 177 " pdb=" CZ PHE D 182 " model vdw 2.204 3.760 nonbonded pdb=" N ASN I 50 " pdb=" CA GLY J 62 " model vdw 2.208 3.520 ... (remaining 137992 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.008 0.075 18044 Z= 0.415 Angle : 1.250 15.872 24450 Z= 0.773 Chirality : 0.061 0.331 2966 Planarity : 0.007 0.085 3102 Dihedral : 18.193 89.250 6546 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 1.57 % Allowed : 11.15 % Favored : 87.28 % Rotamer: Outliers : 9.39 % Allowed : 12.59 % Favored : 78.01 % Cbeta Deviations : 0.09 % 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: -5.80 (0.12), residues: 2350 helix: -4.30 (0.08), residues: 978 sheet: -2.41 (0.29), residues: 273 loop : -3.75 (0.14), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 193 TYR 0.029 0.003 TYR I 145 PHE 0.023 0.002 PHE G 84 TRP 0.008 0.002 TRP D 146 HIS 0.006 0.002 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00822 (18044) covalent geometry : angle 1.24956 (24450) hydrogen bonds : bond 0.30485 ( 651) hydrogen bonds : angle 11.16943 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 409 time to evaluate : 0.703 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 51 MET cc_start: 0.8487 (mmt) cc_final: 0.8273 (mmm) REVERT: A 186 MET cc_start: 0.8586 (ttp) cc_final: 0.8311 (ttp) REVERT: B 135 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: C 42 ASP cc_start: 0.7619 (t70) cc_final: 0.7366 (m-30) REVERT: C 47 GLU cc_start: 0.7404 (pm20) cc_final: 0.6934 (pm20) REVERT: C 50 ASN cc_start: 0.9008 (p0) cc_final: 0.8310 (p0) REVERT: C 81 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8725 (mtmm) REVERT: D 80 SER cc_start: 0.5213 (OUTLIER) cc_final: 0.4659 (t) REVERT: D 168 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7357 (mptt) REVERT: E 26 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5593 (mtt90) REVERT: E 71 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7857 (mm) REVERT: E 75 LYS cc_start: 0.8400 (mmmm) cc_final: 0.7894 (tptm) REVERT: E 85 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8064 (tp) REVERT: E 172 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8643 (mpp) REVERT: E 174 ASP cc_start: 0.7107 (t0) cc_final: 0.6815 (t70) REVERT: E 222 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7921 (t) REVERT: E 227 LYS cc_start: 0.8515 (mttp) cc_final: 0.8312 (mmtt) REVERT: E 252 SER cc_start: 0.6700 (OUTLIER) cc_final: 0.6276 (m) REVERT: E 258 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: F 10 VAL cc_start: 0.8514 (p) cc_final: 0.8141 (m) REVERT: F 35 THR cc_start: 0.6339 (OUTLIER) cc_final: 0.6082 (m) REVERT: F 58 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8734 (p) REVERT: F 73 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7149 (tppt) REVERT: G 96 GLU cc_start: 0.8182 (pt0) cc_final: 0.7541 (pm20) REVERT: G 100 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8618 (mt-10) REVERT: G 169 TYR cc_start: 0.7630 (m-80) cc_final: 0.7424 (m-10) REVERT: H 171 LYS cc_start: 0.8526 (mptt) cc_final: 0.8270 (mmmt) REVERT: I 134 MET cc_start: 0.7688 (mtt) cc_final: 0.7393 (mtt) REVERT: J 6 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7850 (m) REVERT: J 135 ASN cc_start: 0.8441 (p0) cc_final: 0.7975 (t0) REVERT: J 183 MET cc_start: 0.7796 (mpp) cc_final: 0.7501 (mtm) REVERT: K 147 MET cc_start: 0.7702 (ptm) cc_final: 0.7291 (ttt) REVERT: L 8 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7091 (pt) REVERT: L 17 PHE cc_start: 0.7490 (t80) cc_final: 0.7221 (t80) REVERT: L 187 ASP cc_start: 0.8241 (p0) cc_final: 0.7889 (p0) outliers start: 176 outliers final: 47 residues processed: 523 average time/residue: 0.1503 time to fit residues: 115.1604 Evaluate side-chains 323 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 40 GLN C 6 ASN D 139 GLN E 35 ASN E 40 GLN F 23 GLN F 34 GLN F 59 GLN H 35 ASN H 129 GLN I 45 GLN I 180 GLN J 45 GLN L 45 GLN L 97 GLN L 129 GLN L 133 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082301 restraints weight = 54224.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081248 restraints weight = 42453.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081927 restraints weight = 37084.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082179 restraints weight = 30566.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082329 restraints weight = 28677.238| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18044 Z= 0.206 Angle : 0.796 9.255 24450 Z= 0.421 Chirality : 0.046 0.206 2966 Planarity : 0.005 0.079 3102 Dihedral : 11.292 64.919 2680 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.21 % Favored : 89.53 % Rotamer: Outliers : 5.66 % Allowed : 18.62 % Favored : 75.72 % 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: -4.39 (0.14), residues: 2350 helix: -2.61 (0.13), residues: 1030 sheet: -1.89 (0.31), residues: 275 loop : -3.49 (0.15), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 193 TYR 0.016 0.002 TYR E 266 PHE 0.022 0.002 PHE J 93 TRP 0.017 0.002 TRP D 212 HIS 0.011 0.002 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00452 (18044) covalent geometry : angle 0.79613 (24450) hydrogen bonds : bond 0.05861 ( 651) hydrogen bonds : angle 6.24668 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 303 time to evaluate : 0.490 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 138 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8254 (ttmm) REVERT: A 186 MET cc_start: 0.7771 (ttp) cc_final: 0.7516 (ttp) REVERT: A 246 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 135 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: B 237 LEU cc_start: 0.7479 (mm) cc_final: 0.6954 (tp) REVERT: C 36 SER cc_start: 0.6862 (OUTLIER) cc_final: 0.6489 (p) REVERT: C 47 GLU cc_start: 0.7129 (pm20) cc_final: 0.6836 (pm20) REVERT: C 50 ASN cc_start: 0.9080 (p0) cc_final: 0.8659 (p0) REVERT: C 81 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8824 (mtmm) REVERT: D 83 MET cc_start: 0.6445 (ptp) cc_final: 0.4175 (mmp) REVERT: D 129 MET cc_start: 0.7785 (ttm) cc_final: 0.7579 (mtt) REVERT: D 168 LYS cc_start: 0.7811 (tmtt) cc_final: 0.6915 (mmtt) REVERT: E 71 LEU cc_start: 0.8305 (mt) cc_final: 0.8000 (mm) REVERT: E 75 LYS cc_start: 0.8391 (mmmm) cc_final: 0.8084 (tptm) REVERT: F 10 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8310 (m) REVERT: F 35 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.5030 (m) REVERT: G 96 GLU cc_start: 0.8001 (pt0) cc_final: 0.7527 (pm20) REVERT: G 100 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 4 ARG cc_start: 0.7802 (tmm160) cc_final: 0.7542 (ttp80) REVERT: I 102 GLN cc_start: 0.8184 (tt0) cc_final: 0.7796 (tt0) REVERT: I 134 MET cc_start: 0.7649 (mtt) cc_final: 0.7419 (mtt) REVERT: J 60 MET cc_start: 0.7284 (tpt) cc_final: 0.7039 (tpt) REVERT: J 96 GLU cc_start: 0.7483 (mp0) cc_final: 0.7250 (mp0) REVERT: J 104 ASN cc_start: 0.7284 (t0) cc_final: 0.6972 (p0) REVERT: J 135 ASN cc_start: 0.8532 (p0) cc_final: 0.7903 (t0) REVERT: J 169 TYR cc_start: 0.7603 (m-80) cc_final: 0.7373 (m-80) REVERT: J 186 GLU cc_start: 0.8287 (tp30) cc_final: 0.8051 (tp30) outliers start: 106 outliers final: 62 residues processed: 381 average time/residue: 0.1242 time to fit residues: 73.4919 Evaluate side-chains 319 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 229 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 189 optimal weight: 0.0020 chunk 126 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN H 50 ASN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN K 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081243 restraints weight = 55114.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080450 restraints weight = 43633.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081174 restraints weight = 37691.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081388 restraints weight = 30710.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081468 restraints weight = 29087.719| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18044 Z= 0.212 Angle : 0.750 10.711 24450 Z= 0.392 Chirality : 0.045 0.196 2966 Planarity : 0.005 0.073 3102 Dihedral : 9.657 65.773 2604 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.30 % Favored : 89.53 % Rotamer: Outliers : 6.14 % Allowed : 21.34 % Favored : 72.52 % 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: -3.79 (0.15), residues: 2350 helix: -1.87 (0.14), residues: 1048 sheet: -1.88 (0.31), residues: 270 loop : -3.38 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 55 TYR 0.015 0.002 TYR I 158 PHE 0.016 0.002 PHE A 248 TRP 0.010 0.001 TRP D 212 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00473 (18044) covalent geometry : angle 0.75025 (24450) hydrogen bonds : bond 0.04959 ( 651) hydrogen bonds : angle 5.72485 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 270 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: A 104 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8752 (mt) REVERT: A 138 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8278 (ttmm) REVERT: A 246 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: B 135 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 154 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6719 (ttm) REVERT: C 47 GLU cc_start: 0.7133 (pm20) cc_final: 0.6698 (pm20) REVERT: C 50 ASN cc_start: 0.9110 (p0) cc_final: 0.8725 (p0) REVERT: D 104 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8363 (mp) REVERT: D 129 MET cc_start: 0.7843 (ttm) cc_final: 0.7535 (mtt) REVERT: D 168 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7177 (mptt) REVERT: E 20 SER cc_start: 0.6510 (OUTLIER) cc_final: 0.6236 (p) REVERT: E 71 LEU cc_start: 0.8433 (mt) cc_final: 0.8033 (mm) REVERT: F 10 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8148 (m) REVERT: F 24 TYR cc_start: 0.7722 (t80) cc_final: 0.7516 (t80) REVERT: F 28 LEU cc_start: 0.9109 (pp) cc_final: 0.8672 (tp) REVERT: G 96 GLU cc_start: 0.7970 (pt0) cc_final: 0.7631 (pm20) REVERT: G 170 LEU cc_start: 0.8384 (mt) cc_final: 0.7881 (mt) REVERT: H 4 ARG cc_start: 0.7910 (tmm160) cc_final: 0.7683 (ttp80) REVERT: I 134 MET cc_start: 0.7724 (mtt) cc_final: 0.7496 (mtt) REVERT: J 96 GLU cc_start: 0.7561 (mp0) cc_final: 0.6977 (mp0) REVERT: J 97 GLN cc_start: 0.7923 (mp10) cc_final: 0.7018 (mp10) REVERT: J 135 ASN cc_start: 0.8481 (p0) cc_final: 0.7864 (t0) REVERT: J 169 TYR cc_start: 0.7669 (m-80) cc_final: 0.7328 (m-80) REVERT: J 186 GLU cc_start: 0.8361 (tp30) cc_final: 0.8051 (tp30) REVERT: K 142 GLU cc_start: 0.8395 (pt0) cc_final: 0.8162 (pt0) REVERT: K 180 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: L 36 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7181 (mt) outliers start: 115 outliers final: 71 residues processed: 356 average time/residue: 0.1279 time to fit residues: 70.7179 Evaluate side-chains 324 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 243 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 0.0020 chunk 163 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN L 50 ASN L 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.105139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084982 restraints weight = 54265.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083805 restraints weight = 42908.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084639 restraints weight = 39656.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085009 restraints weight = 28783.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085148 restraints weight = 26613.566| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18044 Z= 0.121 Angle : 0.674 11.102 24450 Z= 0.346 Chirality : 0.043 0.162 2966 Planarity : 0.004 0.069 3102 Dihedral : 8.962 66.678 2593 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 4.54 % Allowed : 22.89 % Favored : 72.57 % 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: -3.19 (0.16), residues: 2350 helix: -1.27 (0.15), residues: 1033 sheet: -1.61 (0.33), residues: 264 loop : -3.15 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 9 TYR 0.013 0.001 TYR E 29 PHE 0.022 0.001 PHE A 248 TRP 0.008 0.001 TRP A 146 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00256 (18044) covalent geometry : angle 0.67386 (24450) hydrogen bonds : bond 0.03908 ( 651) hydrogen bonds : angle 5.01430 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 285 time to evaluate : 0.699 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: A 9 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: A 95 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 138 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8264 (ttmm) REVERT: A 213 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8944 (tp) REVERT: B 135 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: C 5 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8118 (mm) REVERT: C 16 ASP cc_start: 0.8778 (p0) cc_final: 0.8481 (p0) REVERT: C 47 GLU cc_start: 0.7122 (pm20) cc_final: 0.6666 (pm20) REVERT: C 50 ASN cc_start: 0.9032 (p0) cc_final: 0.8734 (p0) REVERT: D 70 GLN cc_start: 0.8091 (mm110) cc_final: 0.7760 (mm110) REVERT: D 83 MET cc_start: 0.5208 (ptp) cc_final: 0.3884 (mmp) REVERT: D 120 MET cc_start: 0.8873 (mtt) cc_final: 0.8542 (mtp) REVERT: D 168 LYS cc_start: 0.7917 (tmtt) cc_final: 0.7081 (mptt) REVERT: E 185 LYS cc_start: 0.8062 (mttt) cc_final: 0.7762 (mttt) REVERT: F 10 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8263 (m) REVERT: F 24 TYR cc_start: 0.7589 (t80) cc_final: 0.7383 (t80) REVERT: F 28 LEU cc_start: 0.9054 (pp) cc_final: 0.8711 (mt) REVERT: G 67 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6670 (ttm110) REVERT: G 96 GLU cc_start: 0.7915 (pt0) cc_final: 0.7570 (pm20) REVERT: G 170 LEU cc_start: 0.8365 (mt) cc_final: 0.7859 (mt) REVERT: H 4 ARG cc_start: 0.7816 (tmm160) cc_final: 0.7578 (ttp80) REVERT: H 35 ASN cc_start: 0.8037 (p0) cc_final: 0.7816 (p0) REVERT: I 50 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7439 (m110) REVERT: J 97 GLN cc_start: 0.7671 (mp10) cc_final: 0.6991 (mp10) REVERT: J 135 ASN cc_start: 0.8404 (p0) cc_final: 0.7977 (t0) REVERT: J 186 GLU cc_start: 0.8140 (tp30) cc_final: 0.7891 (tp30) outliers start: 85 outliers final: 48 residues processed: 348 average time/residue: 0.1381 time to fit residues: 73.1766 Evaluate side-chains 310 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 187 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN L 50 ASN L 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081590 restraints weight = 54893.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080544 restraints weight = 46034.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081306 restraints weight = 40777.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081583 restraints weight = 30833.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081741 restraints weight = 28989.536| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18044 Z= 0.212 Angle : 0.728 10.991 24450 Z= 0.376 Chirality : 0.045 0.193 2966 Planarity : 0.004 0.067 3102 Dihedral : 8.959 66.416 2590 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 5.82 % Allowed : 23.64 % Favored : 70.54 % 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: -3.15 (0.16), residues: 2350 helix: -1.13 (0.15), residues: 1049 sheet: -1.69 (0.33), residues: 266 loop : -3.25 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 234 TYR 0.014 0.002 TYR H 145 PHE 0.021 0.002 PHE B 244 TRP 0.008 0.001 TRP A 146 HIS 0.005 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00480 (18044) covalent geometry : angle 0.72813 (24450) hydrogen bonds : bond 0.04315 ( 651) hydrogen bonds : angle 5.19541 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 255 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: A 44 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8123 (tp40) REVERT: A 70 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8540 (mm-40) REVERT: A 138 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8367 (ttmm) REVERT: A 213 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8875 (tp) REVERT: B 135 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: B 154 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6635 (ttm) REVERT: C 47 GLU cc_start: 0.7299 (pm20) cc_final: 0.6813 (pm20) REVERT: C 50 ASN cc_start: 0.9090 (p0) cc_final: 0.8701 (p0) REVERT: D 83 MET cc_start: 0.5076 (ptp) cc_final: 0.3117 (mmp) REVERT: D 90 LEU cc_start: 0.6852 (mm) cc_final: 0.6649 (mm) REVERT: D 104 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8287 (mp) REVERT: D 168 LYS cc_start: 0.7989 (tmtt) cc_final: 0.7235 (mptt) REVERT: F 28 LEU cc_start: 0.9030 (pp) cc_final: 0.8666 (mt) REVERT: G 96 GLU cc_start: 0.8041 (pt0) cc_final: 0.7548 (pm20) REVERT: G 156 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7239 (tm-30) REVERT: G 170 LEU cc_start: 0.8338 (mt) cc_final: 0.7899 (mt) REVERT: I 50 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7517 (m110) REVERT: I 134 MET cc_start: 0.7169 (mtt) cc_final: 0.6805 (ptp) REVERT: J 96 GLU cc_start: 0.7581 (mp0) cc_final: 0.7173 (mp0) REVERT: J 97 GLN cc_start: 0.7885 (mp10) cc_final: 0.6821 (mp10) REVERT: J 135 ASN cc_start: 0.8425 (p0) cc_final: 0.7985 (t0) REVERT: J 186 GLU cc_start: 0.8177 (tp30) cc_final: 0.7865 (tp30) REVERT: K 147 MET cc_start: 0.7961 (tpt) cc_final: 0.7199 (tpt) REVERT: L 23 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (t80) outliers start: 109 outliers final: 81 residues processed: 339 average time/residue: 0.1309 time to fit residues: 68.9572 Evaluate side-chains 334 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 245 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 101 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 150 optimal weight: 0.0040 chunk 48 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN H 35 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.085753 restraints weight = 53750.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084809 restraints weight = 41911.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085635 restraints weight = 35714.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085947 restraints weight = 27689.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086058 restraints weight = 25621.739| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18044 Z= 0.118 Angle : 0.660 11.374 24450 Z= 0.336 Chirality : 0.042 0.167 2966 Planarity : 0.004 0.065 3102 Dihedral : 8.520 70.393 2588 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.00 % Allowed : 25.40 % Favored : 70.60 % 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: -2.71 (0.16), residues: 2350 helix: -0.63 (0.16), residues: 1030 sheet: -1.60 (0.32), residues: 274 loop : -3.10 (0.16), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 4 TYR 0.012 0.001 TYR L 145 PHE 0.028 0.001 PHE A 248 TRP 0.007 0.001 TRP A 146 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00253 (18044) covalent geometry : angle 0.65983 (24450) hydrogen bonds : bond 0.03496 ( 651) hydrogen bonds : angle 4.61806 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 0.697 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: A 44 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7925 (tp40) REVERT: A 95 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 138 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8289 (ttmm) REVERT: B 146 MET cc_start: 0.7328 (mmm) cc_final: 0.6955 (mmm) REVERT: C 47 GLU cc_start: 0.7224 (pm20) cc_final: 0.6775 (pm20) REVERT: C 50 ASN cc_start: 0.9008 (p0) cc_final: 0.8684 (p0) REVERT: D 95 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7084 (pt0) REVERT: D 104 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 120 MET cc_start: 0.8781 (mtt) cc_final: 0.8455 (mtp) REVERT: D 168 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7044 (mptt) REVERT: E 101 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7230 (mt) REVERT: F 24 TYR cc_start: 0.7226 (t80) cc_final: 0.6899 (t80) REVERT: F 28 LEU cc_start: 0.9095 (pp) cc_final: 0.8720 (mt) REVERT: G 67 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6725 (ttm110) REVERT: G 96 GLU cc_start: 0.7975 (pt0) cc_final: 0.7530 (pm20) REVERT: G 170 LEU cc_start: 0.8238 (mt) cc_final: 0.7784 (mt) REVERT: I 50 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7508 (m110) REVERT: J 15 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7826 (tp) REVERT: J 96 GLU cc_start: 0.7530 (mp0) cc_final: 0.7152 (mp0) REVERT: J 97 GLN cc_start: 0.7898 (mp10) cc_final: 0.6744 (mp10) REVERT: J 104 ASN cc_start: 0.7532 (t0) cc_final: 0.7222 (m-40) REVERT: J 135 ASN cc_start: 0.8359 (p0) cc_final: 0.8027 (t0) REVERT: J 186 GLU cc_start: 0.8190 (tp30) cc_final: 0.7865 (tp30) outliers start: 75 outliers final: 51 residues processed: 327 average time/residue: 0.1295 time to fit residues: 65.1904 Evaluate side-chains 307 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 45 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 203 optimal weight: 0.0670 chunk 168 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 206 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084132 restraints weight = 54192.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082725 restraints weight = 45892.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083489 restraints weight = 41482.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083898 restraints weight = 30796.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084039 restraints weight = 27925.774| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18044 Z= 0.146 Angle : 0.680 10.884 24450 Z= 0.347 Chirality : 0.043 0.169 2966 Planarity : 0.004 0.064 3102 Dihedral : 8.175 68.030 2579 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.28 % Favored : 90.68 % Rotamer: Outliers : 4.59 % Allowed : 25.35 % Favored : 70.06 % 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: -2.61 (0.16), residues: 2350 helix: -0.55 (0.16), residues: 1032 sheet: -1.67 (0.32), residues: 268 loop : -3.02 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 57 TYR 0.017 0.001 TYR H 169 PHE 0.026 0.001 PHE B 244 TRP 0.007 0.001 TRP A 146 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00331 (18044) covalent geometry : angle 0.67951 (24450) hydrogen bonds : bond 0.03665 ( 651) hydrogen bonds : angle 4.73970 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 262 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8028 (tp40) REVERT: A 104 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 138 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8306 (ttmm) REVERT: B 237 LEU cc_start: 0.6928 (mm) cc_final: 0.6254 (tp) REVERT: C 47 GLU cc_start: 0.7219 (pm20) cc_final: 0.6762 (pm20) REVERT: C 50 ASN cc_start: 0.9083 (p0) cc_final: 0.8683 (p0) REVERT: D 95 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7090 (pt0) REVERT: D 104 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8246 (mp) REVERT: D 120 MET cc_start: 0.8815 (mtt) cc_final: 0.8506 (mtp) REVERT: D 168 LYS cc_start: 0.7967 (tmtt) cc_final: 0.7171 (mptt) REVERT: F 24 TYR cc_start: 0.7303 (t80) cc_final: 0.7000 (t80) REVERT: F 28 LEU cc_start: 0.9110 (pp) cc_final: 0.8732 (mt) REVERT: G 103 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8142 (mmtm) REVERT: G 170 LEU cc_start: 0.8189 (mt) cc_final: 0.7787 (mt) REVERT: I 50 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7533 (m110) REVERT: J 15 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7891 (tp) REVERT: J 97 GLN cc_start: 0.7934 (mp10) cc_final: 0.6827 (mp10) REVERT: J 99 LYS cc_start: 0.9296 (mmtm) cc_final: 0.9059 (mppt) REVERT: J 104 ASN cc_start: 0.7549 (t0) cc_final: 0.7236 (m-40) REVERT: J 135 ASN cc_start: 0.8312 (p0) cc_final: 0.8040 (t0) REVERT: J 186 GLU cc_start: 0.8195 (tp30) cc_final: 0.7832 (tp30) REVERT: L 23 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7741 (t80) outliers start: 86 outliers final: 67 residues processed: 327 average time/residue: 0.1269 time to fit residues: 64.3967 Evaluate side-chains 321 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.102934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082267 restraints weight = 54307.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081187 restraints weight = 48640.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081836 restraints weight = 43371.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082297 restraints weight = 32617.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082394 restraints weight = 28992.111| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18044 Z= 0.184 Angle : 0.721 10.864 24450 Z= 0.367 Chirality : 0.044 0.227 2966 Planarity : 0.004 0.064 3102 Dihedral : 8.167 71.410 2579 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.04 % Favored : 89.87 % Rotamer: Outliers : 5.44 % Allowed : 25.08 % Favored : 69.48 % 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: -2.63 (0.16), residues: 2350 helix: -0.55 (0.16), residues: 1024 sheet: -1.73 (0.32), residues: 272 loop : -3.03 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 4 TYR 0.013 0.002 TYR H 145 PHE 0.019 0.002 PHE A 41 TRP 0.009 0.001 TRP A 146 HIS 0.004 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00418 (18044) covalent geometry : angle 0.72077 (24450) hydrogen bonds : bond 0.04020 ( 651) hydrogen bonds : angle 4.89534 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 254 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8059 (tp40) REVERT: A 104 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 138 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8332 (ttmm) REVERT: C 47 GLU cc_start: 0.7281 (pm20) cc_final: 0.6711 (pm20) REVERT: D 104 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8252 (mp) REVERT: D 120 MET cc_start: 0.8873 (mtt) cc_final: 0.8440 (mtp) REVERT: D 168 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7337 (mptt) REVERT: D 254 MET cc_start: 0.8006 (ppp) cc_final: 0.7793 (tmm) REVERT: F 24 TYR cc_start: 0.7450 (t80) cc_final: 0.7143 (t80) REVERT: F 28 LEU cc_start: 0.9116 (pp) cc_final: 0.8705 (tp) REVERT: G 67 ARG cc_start: 0.7275 (mtm110) cc_final: 0.6740 (ttm110) REVERT: G 103 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8314 (mmtm) REVERT: G 170 LEU cc_start: 0.8253 (mt) cc_final: 0.7851 (mt) REVERT: H 26 MET cc_start: 0.7706 (tpp) cc_final: 0.7483 (tpp) REVERT: I 50 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (m-40) REVERT: J 15 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (tp) REVERT: J 97 GLN cc_start: 0.7939 (mp10) cc_final: 0.7204 (mp10) REVERT: J 104 ASN cc_start: 0.7530 (t0) cc_final: 0.7280 (m-40) REVERT: K 142 GLU cc_start: 0.8296 (pt0) cc_final: 0.7947 (pm20) REVERT: L 23 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7743 (t80) outliers start: 102 outliers final: 84 residues processed: 335 average time/residue: 0.1201 time to fit residues: 63.1480 Evaluate side-chains 335 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 245 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 52 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 75 optimal weight: 0.0770 chunk 109 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 188 optimal weight: 0.0030 chunk 121 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.1552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085049 restraints weight = 53835.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083699 restraints weight = 46747.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084509 restraints weight = 39050.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084756 restraints weight = 31790.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084894 restraints weight = 29690.138| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18044 Z= 0.123 Angle : 0.696 11.018 24450 Z= 0.350 Chirality : 0.043 0.236 2966 Planarity : 0.004 0.063 3102 Dihedral : 7.911 74.487 2579 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.68 % Favored : 91.23 % Rotamer: Outliers : 4.11 % Allowed : 26.89 % Favored : 69.00 % 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: -2.45 (0.16), residues: 2350 helix: -0.35 (0.16), residues: 1029 sheet: -1.65 (0.32), residues: 270 loop : -3.00 (0.16), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 9 TYR 0.012 0.001 TYR L 145 PHE 0.028 0.001 PHE B 244 TRP 0.015 0.001 TRP F 60 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00272 (18044) covalent geometry : angle 0.69647 (24450) hydrogen bonds : bond 0.03537 ( 651) hydrogen bonds : angle 4.60468 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 264 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: A 95 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 138 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8332 (ttmm) REVERT: C 47 GLU cc_start: 0.7207 (pm20) cc_final: 0.6682 (pm20) REVERT: D 62 PHE cc_start: 0.8349 (m-10) cc_final: 0.8020 (m-80) REVERT: D 83 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.3675 (ptp) REVERT: D 90 LEU cc_start: 0.6783 (mm) cc_final: 0.6411 (mm) REVERT: D 95 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6931 (pt0) REVERT: D 104 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8103 (mp) REVERT: D 120 MET cc_start: 0.8668 (mtt) cc_final: 0.8346 (mtp) REVERT: D 168 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7239 (mptt) REVERT: D 254 MET cc_start: 0.8009 (ppp) cc_final: 0.7738 (tmm) REVERT: F 24 TYR cc_start: 0.7282 (t80) cc_final: 0.6925 (t80) REVERT: F 28 LEU cc_start: 0.9221 (pp) cc_final: 0.8837 (mt) REVERT: G 93 PHE cc_start: 0.6705 (p90) cc_final: 0.6452 (p90) REVERT: G 103 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8147 (mmtm) REVERT: G 170 LEU cc_start: 0.8186 (mt) cc_final: 0.7777 (mt) REVERT: H 26 MET cc_start: 0.7744 (tpp) cc_final: 0.7540 (tpp) REVERT: H 171 LYS cc_start: 0.8227 (mptt) cc_final: 0.7979 (mmmt) REVERT: I 50 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: J 15 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7938 (tp) REVERT: J 97 GLN cc_start: 0.7930 (mp10) cc_final: 0.7156 (mp10) REVERT: J 104 ASN cc_start: 0.7700 (t0) cc_final: 0.7446 (m-40) outliers start: 77 outliers final: 66 residues processed: 320 average time/residue: 0.1221 time to fit residues: 61.9253 Evaluate side-chains 325 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 254 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 163 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.104288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083825 restraints weight = 54070.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082513 restraints weight = 48096.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083323 restraints weight = 41460.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083643 restraints weight = 31840.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083774 restraints weight = 28945.979| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18044 Z= 0.152 Angle : 0.721 11.001 24450 Z= 0.361 Chirality : 0.044 0.233 2966 Planarity : 0.004 0.063 3102 Dihedral : 7.841 72.614 2576 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.40 % Favored : 90.51 % Rotamer: Outliers : 4.32 % Allowed : 26.63 % Favored : 69.05 % 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: -2.38 (0.17), residues: 2350 helix: -0.28 (0.17), residues: 1026 sheet: -1.66 (0.32), residues: 270 loop : -2.94 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 4 TYR 0.013 0.001 TYR A 238 PHE 0.023 0.001 PHE A 41 TRP 0.025 0.002 TRP F 60 HIS 0.003 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00348 (18044) covalent geometry : angle 0.72087 (24450) hydrogen bonds : bond 0.03653 ( 651) hydrogen bonds : angle 4.68188 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 258 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8051 (tp40) REVERT: A 138 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8341 (ttmm) REVERT: B 80 MET cc_start: 0.5485 (mmp) cc_final: 0.5133 (mmp) REVERT: C 47 GLU cc_start: 0.7267 (pm20) cc_final: 0.6704 (pm20) REVERT: D 62 PHE cc_start: 0.8418 (m-10) cc_final: 0.8111 (m-80) REVERT: D 104 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8141 (mp) REVERT: D 120 MET cc_start: 0.8751 (mtt) cc_final: 0.8448 (mtp) REVERT: D 168 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7159 (mptt) REVERT: F 24 TYR cc_start: 0.7366 (t80) cc_final: 0.7099 (t80) REVERT: F 28 LEU cc_start: 0.9119 (pp) cc_final: 0.8741 (tp) REVERT: G 96 GLU cc_start: 0.8405 (tp30) cc_final: 0.7602 (tm-30) REVERT: G 100 GLU cc_start: 0.8680 (mt-10) cc_final: 0.7260 (mt-10) REVERT: G 103 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8174 (mmtm) REVERT: G 170 LEU cc_start: 0.8162 (mt) cc_final: 0.7763 (mt) REVERT: I 50 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: J 15 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7929 (tp) REVERT: J 97 GLN cc_start: 0.7993 (mp10) cc_final: 0.7208 (mp10) REVERT: J 104 ASN cc_start: 0.7674 (t0) cc_final: 0.7400 (m-40) REVERT: L 23 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7673 (t80) outliers start: 81 outliers final: 72 residues processed: 317 average time/residue: 0.1226 time to fit residues: 61.4935 Evaluate side-chains 331 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 30.0000 chunk 226 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 69 optimal weight: 0.0010 chunk 118 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 HIS H 35 ASN I 97 GLN K 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.105523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085185 restraints weight = 54071.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084088 restraints weight = 42799.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085165 restraints weight = 39205.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085269 restraints weight = 29895.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085398 restraints weight = 26322.738| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18044 Z= 0.127 Angle : 0.710 11.557 24450 Z= 0.354 Chirality : 0.043 0.231 2966 Planarity : 0.004 0.063 3102 Dihedral : 7.712 74.820 2576 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 4.11 % Allowed : 26.95 % Favored : 68.94 % 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: -2.28 (0.17), residues: 2350 helix: -0.17 (0.17), residues: 1026 sheet: -1.57 (0.32), residues: 270 loop : -2.93 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 4 TYR 0.012 0.001 TYR L 145 PHE 0.029 0.001 PHE B 244 TRP 0.028 0.002 TRP F 60 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00286 (18044) covalent geometry : angle 0.70978 (24450) hydrogen bonds : bond 0.03466 ( 651) hydrogen bonds : angle 4.51798 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.69 seconds wall clock time: 47 minutes 5.92 seconds (2825.92 seconds total)