Starting phenix.real_space_refine on Sat Jul 4 01:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d09_30527/07_2026/7d09_30527.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.14, per 1000 atoms: 0.23 Number of scatterers: 17802 At special positions: 0 Unit cell: (131.527, 121.744, 148.919, 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: 1.59 Conformation dependent library (CDL) restraints added in 800.6 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: 93 helices and 17 sheets defined 46.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 30 removed outlier: 3.609A pdb=" N GLU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 28 " --> pdb=" O MET A 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.815A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.534A pdb=" N SER A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.580A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.868A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.649A pdb=" N MET A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.568A pdb=" N VAL A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.936A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.670A pdb=" N MET A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.633A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.717A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 3.643A pdb=" N LEU B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.632A pdb=" N HIS B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.963A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.977A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 200 removed outlier: 3.814A pdb=" N ARG B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.607A pdb=" N SER B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.563A pdb=" N THR B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.788A pdb=" N GLN C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 removed outlier: 3.511A pdb=" N LEU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'D' and resid 2 through 30 removed outlier: 3.541A pdb=" N GLU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 28 " --> pdb=" O MET D 24 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.814A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.555A pdb=" N ILE D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.534A pdb=" N SER D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 93 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 3.580A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 123 removed outlier: 3.868A pdb=" N LEU D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.648A pdb=" N MET D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.567A pdb=" N VAL D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 172 removed outlier: 3.935A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.670A pdb=" N MET D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 220 removed outlier: 3.634A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.717A pdb=" N SER D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.643A pdb=" N LEU E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.633A pdb=" N HIS E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.963A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 135 " --> pdb=" O ALA E 131 " (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: 4.105A pdb=" N ARG E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 200 removed outlier: 3.814A pdb=" N ARG E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.606A pdb=" N SER E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 217 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.563A pdb=" N THR E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.789A pdb=" N GLN F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.511A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'G' and resid 4 through 26 removed outlier: 3.555A pdb=" N GLY G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 101 Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.630A pdb=" N ALA G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 133 removed outlier: 3.576A pdb=" N GLN G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 193 Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.729A pdb=" N VAL H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 30 removed outlier: 3.577A pdb=" N SER H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 30 " --> pdb=" O MET H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 94 through 110 removed outlier: 3.949A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU H 106 " --> pdb=" O GLN H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 124 through 132 removed outlier: 3.988A pdb=" N GLN H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 4.198A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 192 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 28 removed outlier: 3.731A pdb=" N VAL I 10 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL I 28 " --> pdb=" O LEU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 101 removed outlier: 4.075A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 108 removed outlier: 3.835A pdb=" N ASP I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 119 removed outlier: 3.668A pdb=" N THR I 119 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 132 removed outlier: 4.328A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 192 removed outlier: 4.385A pdb=" N SER I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.620A pdb=" N ILE J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 removed outlier: 3.837A pdb=" N LEU J 98 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS J 99 " --> pdb=" O GLU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 123 through 132 removed outlier: 4.495A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.604A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 23 removed outlier: 4.378A pdb=" N VAL K 14 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 106 removed outlier: 3.680A pdb=" N VAL K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 134 removed outlier: 3.771A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER K 132 " --> pdb=" O GLN K 128 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET K 134 " --> pdb=" O LEU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.666A pdb=" N LEU K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE K 193 " --> pdb=" O ILE K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.501A pdb=" N PHE L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 21 " --> pdb=" O PHE L 17 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 92 removed outlier: 3.519A pdb=" N THR L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 removed outlier: 3.646A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 110 removed outlier: 3.963A pdb=" N GLU L 108 " --> pdb=" O ASN L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 122 Processing helix chain 'L' and resid 123 through 135 removed outlier: 3.716A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 192 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.373A pdb=" N LEU B 34 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 15 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 69 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.909A pdb=" N ILE B 171 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL B 206 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 173 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 43 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 223 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 45 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 4 removed outlier: 7.612A pdb=" N VAL C 11 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.372A pdb=" N LEU E 34 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU E 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AA8, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.909A pdb=" N ILE E 171 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL E 206 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR E 173 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA E 43 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL E 223 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET E 45 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.893A pdb=" N GLY F 13 " --> pdb=" O GLN F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 68 through 73 removed outlier: 5.985A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR G 83 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ILE G 176 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 66 removed outlier: 6.606A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 149 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 39 through 44 removed outlier: 3.620A pdb=" N TYR H 40 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR H 83 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE H 65 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS H 57 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE H 161 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR H 59 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 41 through 46 removed outlier: 6.171A pdb=" N THR I 81 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE I 71 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR I 83 " --> pdb=" O ASP I 69 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 42 through 44 removed outlier: 4.024A pdb=" N SER J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.738A pdb=" N VAL J 162 " --> pdb=" O TYR J 145 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR J 145 " --> pdb=" O VAL J 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 40 through 44 removed outlier: 3.632A pdb=" N ALA K 44 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE K 71 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR K 83 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR K 158 " --> pdb=" O ALA K 149 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR K 145 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE K 146 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 41 through 44 removed outlier: 3.645A pdb=" N PHE L 84 " --> pdb=" O MET L 42 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU L 79 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1878 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: 2.93 Time building geometry restraints manager: 2.07 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: 5574 1.33 - 1.46: 2726 1.46 - 1.58: 9566 1.58 - 1.70: 10 1.70 - 1.82: 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 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C5 ATP B 301 " pdb=" N7 ATP B 301 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.15e+01 ... (remaining 18039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 24137 3.67 - 7.34: 279 7.34 - 11.01: 30 11.01 - 14.68: 0 14.68 - 18.34: 4 Bond angle restraints: 24450 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 121.53 18.34 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 121.55 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 121.95 14.88 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 121.97 14.86 1.00e+00 1.00e+00 2.21e+02 angle pdb=" C ASP E 209 " pdb=" N VAL E 210 " pdb=" CA VAL E 210 " ideal model delta sigma weight residual 120.24 125.66 -5.42 6.30e-01 2.52e+00 7.41e+01 ... (remaining 24445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9505 17.65 - 35.31: 947 35.31 - 52.96: 222 52.96 - 70.61: 108 70.61 - 88.26: 30 Dihedral angle restraints: 10812 sinusoidal: 4070 harmonic: 6742 Sorted by residual: dihedral pdb=" CA CYS D 221 " pdb=" C CYS D 221 " pdb=" N ASP D 222 " pdb=" CA ASP D 222 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA CYS A 221 " pdb=" C CYS A 221 " pdb=" N ASP A 222 " pdb=" CA ASP A 222 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA G 144 " pdb=" C ALA G 144 " pdb=" N TYR G 145 " pdb=" CA TYR G 145 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 10809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2215 0.056 - 0.112: 575 0.112 - 0.168: 152 0.168 - 0.225: 18 0.225 - 0.281: 6 Chirality restraints: 2966 Sorted by residual: chirality pdb=" CB THR E 142 " pdb=" CA THR E 142 " pdb=" OG1 THR E 142 " pdb=" CG2 THR E 142 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB THR B 142 " pdb=" CA THR B 142 " pdb=" OG1 THR B 142 " pdb=" CG2 THR B 142 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ARG E 140 " pdb=" N ARG E 140 " pdb=" C ARG E 140 " pdb=" CB ARG E 140 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2963 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 51 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C THR C 51 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 51 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU C 52 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 51 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR F 51 " 0.051 2.00e-02 2.50e+03 pdb=" O THR F 51 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 52 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 97 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 98 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.041 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1675 2.72 - 3.27: 16762 3.27 - 3.81: 27568 3.81 - 4.36: 32858 4.36 - 4.90: 56712 Nonbonded interactions: 135575 Sorted by model distance: nonbonded pdb=" N MET G 26 " pdb=" SD MET G 26 " model vdw 2.181 3.480 nonbonded pdb=" CG2 VAL K 76 " pdb=" OE1 GLN L 97 " model vdw 2.222 3.460 nonbonded pdb=" OE2 GLU G 186 " pdb=" OG1 THR H 150 " model vdw 2.234 3.040 nonbonded pdb=" CD1 LEU H 185 " pdb=" CG2 THR I 150 " model vdw 2.241 3.880 nonbonded pdb=" CG1 VAL G 63 " pdb=" CD1 LEU L 73 " model vdw 2.242 3.880 ... (remaining 135570 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: 0.02 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: 0.560 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.790 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 18044 Z= 0.371 Angle : 1.112 18.344 24450 Z= 0.705 Chirality : 0.056 0.281 2966 Planarity : 0.006 0.072 3102 Dihedral : 16.969 88.263 6484 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.28 % Favored : 89.49 % Rotamer: Outliers : 8.59 % Allowed : 10.41 % Favored : 81.00 % 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: -6.00 (0.12), residues: 2350 helix: -4.77 (0.05), residues: 986 sheet: -2.72 (0.27), residues: 301 loop : -3.45 (0.15), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 140 TYR 0.019 0.002 TYR G 40 PHE 0.021 0.002 PHE I 13 TRP 0.019 0.002 TRP A 212 HIS 0.005 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.37 (18044) covalent geometry : angle 1.11181 / 0.70 (24450) hydrogen bonds : bond 0.30783 / 20.34 ( 652) hydrogen bonds : angle 10.82672 / 7.47 ( 1878) *********************** 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 581 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 420 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.5596 (OUTLIER) cc_final: 0.4283 (m) REVERT: A 95 GLU cc_start: 0.8324 (tp30) cc_final: 0.7019 (tt0) REVERT: A 116 GLU cc_start: 0.7629 (tt0) cc_final: 0.7349 (mt-10) REVERT: A 154 MET cc_start: 0.8548 (mtp) cc_final: 0.8347 (mtp) REVERT: A 168 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8838 (tttm) REVERT: B 227 LYS cc_start: 0.8484 (pttp) cc_final: 0.8202 (mptt) REVERT: B 229 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: C 18 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: C 19 ASN cc_start: 0.8261 (p0) cc_final: 0.7977 (p0) REVERT: C 80 LEU cc_start: 0.8879 (pt) cc_final: 0.8275 (pt) REVERT: D 24 MET cc_start: 0.9159 (ttp) cc_final: 0.8881 (ttm) REVERT: D 116 GLU cc_start: 0.7439 (tt0) cc_final: 0.7229 (mt-10) REVERT: D 138 LYS cc_start: 0.8834 (tppt) cc_final: 0.8431 (tttt) REVERT: D 230 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8940 (m) REVERT: D 232 MET cc_start: 0.9008 (mtp) cc_final: 0.8719 (mtm) REVERT: E 135 GLU cc_start: 0.8014 (tp30) cc_final: 0.7630 (tm-30) REVERT: E 169 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: E 229 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (mm110) REVERT: E 246 LYS cc_start: 0.9192 (tttp) cc_final: 0.8349 (pttp) REVERT: F 42 ASP cc_start: 0.7496 (m-30) cc_final: 0.7233 (t0) REVERT: F 43 LEU cc_start: 0.8538 (pt) cc_final: 0.8238 (pp) REVERT: F 73 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7966 (tppt) REVERT: F 78 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8458 (ttpt) REVERT: G 129 GLN cc_start: 0.2527 (tt0) cc_final: 0.1959 (tt0) REVERT: G 168 ASN cc_start: 0.7879 (m110) cc_final: 0.7649 (m110) REVERT: G 192 PHE cc_start: 0.6591 (t80) cc_final: 0.6198 (t80) REVERT: H 85 ASP cc_start: 0.8729 (p0) cc_final: 0.8523 (p0) REVERT: H 143 ASP cc_start: 0.8067 (p0) cc_final: 0.7771 (p0) REVERT: H 183 MET cc_start: 0.5919 (ttp) cc_final: 0.5702 (ttm) REVERT: H 192 PHE cc_start: 0.5639 (t80) cc_final: 0.4962 (t80) REVERT: I 50 ASN cc_start: 0.8622 (m-40) cc_final: 0.7866 (m110) REVERT: J 87 ASP cc_start: 0.7350 (m-30) cc_final: 0.6992 (t70) REVERT: J 180 GLN cc_start: 0.6512 (pt0) cc_final: 0.6090 (pt0) REVERT: K 97 GLN cc_start: 0.6105 (tt0) cc_final: 0.5391 (mm110) REVERT: L 189 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6071 (mm) REVERT: L 191 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.4780 (ptmm) outliers start: 161 outliers final: 37 residues processed: 524 average time/residue: 0.1490 time to fit residues: 115.7579 Evaluate side-chains 354 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 70 GLN A 189 ASN A 198 ASN B 31 ASN B 229 GLN B 263 HIS C 23 GLN C 34 GLN C 45 GLN C 66 GLN C 87 HIS D 46 HIS D 70 GLN D 139 GLN E 31 ASN E 97 GLN E 263 HIS F 45 GLN G 128 GLN H 102 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN K 180 GLN L 129 GLN L 180 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102193 restraints weight = 31535.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102046 restraints weight = 25067.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102711 restraints weight = 26858.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103273 restraints weight = 18530.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103629 restraints weight = 17026.676| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18044 Z= 0.146 Angle : 0.665 8.424 24450 Z= 0.349 Chirality : 0.043 0.178 2966 Planarity : 0.005 0.043 3102 Dihedral : 8.588 77.025 2601 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.57 % Favored : 92.17 % Rotamer: Outliers : 4.16 % Allowed : 15.37 % Favored : 80.47 % 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: -2.85 (0.12), residues: 995 sheet: -2.31 (0.27), residues: 300 loop : -3.08 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 55 TYR 0.018 0.001 TYR E 259 PHE 0.036 0.001 PHE C 37 TRP 0.020 0.001 TRP A 212 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (18044) covalent geometry : angle 0.66451 / 0.35 (24450) hydrogen bonds : bond 0.05208 / 3.46 ( 652) hydrogen bonds : angle 5.87400 / 4.08 ( 1878) *********************** 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 440 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 362 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7288 (m) REVERT: A 27 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: A 45 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7187 (ttt) REVERT: A 87 MET cc_start: 0.7970 (tmm) cc_final: 0.7638 (tmm) REVERT: A 116 GLU cc_start: 0.7539 (tt0) cc_final: 0.7309 (mt-10) REVERT: B 73 ASP cc_start: 0.7373 (m-30) cc_final: 0.6968 (m-30) REVERT: B 75 LYS cc_start: 0.7296 (tttm) cc_final: 0.7077 (tttm) REVERT: C 18 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: C 19 ASN cc_start: 0.8602 (p0) cc_final: 0.8163 (p0) REVERT: D 24 MET cc_start: 0.9179 (ttp) cc_final: 0.8825 (ttm) REVERT: D 116 GLU cc_start: 0.7413 (tt0) cc_final: 0.7048 (mt-10) REVERT: D 230 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9006 (m) REVERT: D 234 ARG cc_start: 0.5979 (ttt180) cc_final: 0.5444 (mtm-85) REVERT: E 246 LYS cc_start: 0.9085 (tttp) cc_final: 0.8399 (pttp) REVERT: F 18 GLU cc_start: 0.8231 (pm20) cc_final: 0.8013 (pm20) REVERT: F 84 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: G 27 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7802 (tppp) REVERT: G 64 THR cc_start: 0.8261 (m) cc_final: 0.8051 (p) REVERT: G 99 LYS cc_start: 0.8195 (mppt) cc_final: 0.7926 (mptt) REVERT: H 134 MET cc_start: 0.6623 (ptp) cc_final: 0.5870 (ttt) REVERT: H 143 ASP cc_start: 0.7824 (p0) cc_final: 0.7609 (p0) REVERT: I 42 MET cc_start: 0.7823 (mtt) cc_final: 0.7595 (mtt) REVERT: I 50 ASN cc_start: 0.8228 (m-40) cc_final: 0.7529 (m110) REVERT: I 141 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: K 7 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: K 97 GLN cc_start: 0.6241 (tt0) cc_final: 0.5785 (tp40) REVERT: L 191 LYS cc_start: 0.5312 (OUTLIER) cc_final: 0.4874 (ptmm) outliers start: 78 outliers final: 36 residues processed: 409 average time/residue: 0.1399 time to fit residues: 86.6302 Evaluate side-chains 343 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 229 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 189 optimal weight: 0.4980 chunk 126 optimal weight: 0.1980 chunk 170 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN C 93 HIS F 48 HIS H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101789 restraints weight = 31590.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101419 restraints weight = 26072.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102114 restraints weight = 27558.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102812 restraints weight = 18823.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103064 restraints weight = 17358.301| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18044 Z= 0.150 Angle : 0.625 8.109 24450 Z= 0.324 Chirality : 0.043 0.170 2966 Planarity : 0.004 0.050 3102 Dihedral : 6.435 57.921 2529 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.43 % Rotamer: Outliers : 3.90 % Allowed : 17.56 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.39 (0.15), residues: 2350 helix: -1.70 (0.15), residues: 1021 sheet: -1.80 (0.30), residues: 283 loop : -2.90 (0.16), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 82 TYR 0.023 0.001 TYR E 259 PHE 0.011 0.001 PHE B 177 TRP 0.016 0.001 TRP A 212 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18044) covalent geometry : angle 0.62517 / 0.32 (24450) hydrogen bonds : bond 0.04244 / 2.81 ( 652) hydrogen bonds : angle 5.22908 / 3.63 ( 1878) *********************** 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 394 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 198 ASN cc_start: 0.8430 (m-40) cc_final: 0.8187 (m-40) REVERT: C 19 ASN cc_start: 0.8487 (p0) cc_final: 0.8156 (p0) REVERT: C 91 ASP cc_start: 0.8281 (t0) cc_final: 0.7870 (t0) REVERT: D 24 MET cc_start: 0.9192 (ttp) cc_final: 0.8811 (ttm) REVERT: D 116 GLU cc_start: 0.7506 (tt0) cc_final: 0.7158 (mt-10) REVERT: D 130 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 234 ARG cc_start: 0.6278 (ttt180) cc_final: 0.5636 (mtm-85) REVERT: E 75 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8380 (mmtm) REVERT: E 246 LYS cc_start: 0.9157 (tttp) cc_final: 0.8425 (pttp) REVERT: F 18 GLU cc_start: 0.7876 (pm20) cc_final: 0.7655 (pm20) REVERT: G 64 THR cc_start: 0.8200 (m) cc_final: 0.7982 (p) REVERT: G 99 LYS cc_start: 0.8209 (mppt) cc_final: 0.7928 (mptt) REVERT: G 167 LEU cc_start: 0.8016 (tp) cc_final: 0.7045 (pt) REVERT: I 50 ASN cc_start: 0.8387 (m-40) cc_final: 0.7737 (m110) REVERT: I 60 MET cc_start: 0.8288 (tpp) cc_final: 0.8057 (tpt) REVERT: I 141 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: I 154 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7763 (mp) REVERT: J 192 PHE cc_start: 0.6107 (t80) cc_final: 0.5558 (t80) REVERT: K 7 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: K 97 GLN cc_start: 0.6060 (tt0) cc_final: 0.5257 (mm110) REVERT: L 186 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: L 191 LYS cc_start: 0.5096 (OUTLIER) cc_final: 0.4697 (ptmm) outliers start: 73 outliers final: 47 residues processed: 366 average time/residue: 0.1401 time to fit residues: 77.4802 Evaluate side-chains 345 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN F 23 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN G 180 GLN H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101788 restraints weight = 31578.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101057 restraints weight = 24575.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101621 restraints weight = 27680.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102268 restraints weight = 18642.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102582 restraints weight = 16558.862| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3387 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= 0.143 Angle : 0.609 11.506 24450 Z= 0.312 Chirality : 0.042 0.144 2966 Planarity : 0.003 0.045 3102 Dihedral : 5.975 59.024 2519 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 4.38 % Allowed : 18.94 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.16), residues: 2350 helix: -1.01 (0.16), residues: 1001 sheet: -1.52 (0.31), residues: 283 loop : -2.71 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 82 TYR 0.020 0.001 TYR E 259 PHE 0.035 0.001 PHE C 37 TRP 0.013 0.001 TRP A 212 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (18044) covalent geometry : angle 0.60896 / 0.31 (24450) hydrogen bonds : bond 0.03844 / 2.55 ( 652) hydrogen bonds : angle 4.90939 / 3.39 ( 1878) *********************** 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 392 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 310 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 198 ASN cc_start: 0.8426 (m-40) cc_final: 0.8180 (m-40) REVERT: B 73 ASP cc_start: 0.7384 (m-30) cc_final: 0.7122 (m-30) REVERT: C 19 ASN cc_start: 0.8570 (p0) cc_final: 0.8217 (p0) REVERT: C 91 ASP cc_start: 0.8437 (t0) cc_final: 0.8212 (t0) REVERT: D 24 MET cc_start: 0.9205 (ttp) cc_final: 0.8830 (ttm) REVERT: D 116 GLU cc_start: 0.7441 (tt0) cc_final: 0.7220 (mt-10) REVERT: D 130 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 234 ARG cc_start: 0.6151 (ttt180) cc_final: 0.5443 (mtm-85) REVERT: E 246 LYS cc_start: 0.9148 (tttp) cc_final: 0.8465 (pttp) REVERT: F 18 GLU cc_start: 0.7922 (pm20) cc_final: 0.7688 (pm20) REVERT: F 84 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: G 167 LEU cc_start: 0.7998 (tp) cc_final: 0.7015 (pt) REVERT: G 168 ASN cc_start: 0.8351 (m110) cc_final: 0.7944 (m-40) REVERT: H 45 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7441 (mm110) REVERT: H 96 GLU cc_start: 0.7300 (pm20) cc_final: 0.6966 (pm20) REVERT: H 97 GLN cc_start: 0.6914 (mt0) cc_final: 0.6684 (mt0) REVERT: H 134 MET cc_start: 0.6689 (mtt) cc_final: 0.6001 (ttt) REVERT: I 50 ASN cc_start: 0.8288 (m-40) cc_final: 0.7657 (m110) REVERT: I 141 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: J 143 ASP cc_start: 0.8203 (m-30) cc_final: 0.7051 (t0) REVERT: J 189 ILE cc_start: 0.7578 (mm) cc_final: 0.7274 (tp) REVERT: J 192 PHE cc_start: 0.6035 (t80) cc_final: 0.5488 (t80) REVERT: K 7 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: K 97 GLN cc_start: 0.5924 (tt0) cc_final: 0.5138 (mm110) REVERT: L 191 LYS cc_start: 0.5082 (OUTLIER) cc_final: 0.4603 (ptmm) outliers start: 82 outliers final: 58 residues processed: 366 average time/residue: 0.1342 time to fit residues: 75.7577 Evaluate side-chains 351 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 187 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 185 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 227 optimal weight: 0.1980 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN E 79 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102510 restraints weight = 31443.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102126 restraints weight = 23368.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102671 restraints weight = 24240.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103180 restraints weight = 17504.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103575 restraints weight = 15734.100| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18044 Z= 0.110 Angle : 0.572 9.865 24450 Z= 0.293 Chirality : 0.042 0.195 2966 Planarity : 0.003 0.051 3102 Dihedral : 5.699 59.193 2518 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 3.74 % Allowed : 20.01 % Favored : 76.25 % 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: -2.32 (0.16), residues: 2350 helix: -0.54 (0.16), residues: 994 sheet: -1.33 (0.31), residues: 291 loop : -2.61 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 82 TYR 0.017 0.001 TYR E 259 PHE 0.011 0.001 PHE F 17 TRP 0.009 0.001 TRP A 212 HIS 0.001 0.000 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (18044) covalent geometry : angle 0.57177 / 0.29 (24450) hydrogen bonds : bond 0.03335 / 2.20 ( 652) hydrogen bonds : angle 4.62503 / 3.18 ( 1878) *********************** 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 381 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 198 ASN cc_start: 0.8477 (m-40) cc_final: 0.8252 (m-40) REVERT: C 19 ASN cc_start: 0.8525 (p0) cc_final: 0.8172 (p0) REVERT: D 24 MET cc_start: 0.9155 (ttp) cc_final: 0.8835 (ttm) REVERT: D 130 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 234 ARG cc_start: 0.6115 (ttt180) cc_final: 0.5429 (mtm-85) REVERT: E 246 LYS cc_start: 0.9161 (tttp) cc_final: 0.8464 (pttp) REVERT: G 64 THR cc_start: 0.8092 (m) cc_final: 0.7891 (p) REVERT: G 167 LEU cc_start: 0.8015 (tp) cc_final: 0.6992 (pt) REVERT: G 168 ASN cc_start: 0.8279 (m110) cc_final: 0.7911 (m-40) REVERT: H 45 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7270 (mm110) REVERT: H 134 MET cc_start: 0.6287 (mtt) cc_final: 0.5573 (ttp) REVERT: I 50 ASN cc_start: 0.8391 (m-40) cc_final: 0.7740 (m110) REVERT: I 141 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: J 87 ASP cc_start: 0.6885 (m-30) cc_final: 0.6649 (p0) REVERT: J 143 ASP cc_start: 0.8197 (m-30) cc_final: 0.7041 (t0) REVERT: J 189 ILE cc_start: 0.7748 (mm) cc_final: 0.7443 (tp) REVERT: J 192 PHE cc_start: 0.5998 (t80) cc_final: 0.5450 (t80) REVERT: K 97 GLN cc_start: 0.5862 (tt0) cc_final: 0.5141 (mm110) REVERT: L 70 SER cc_start: 0.5363 (OUTLIER) cc_final: 0.4920 (t) outliers start: 70 outliers final: 50 residues processed: 358 average time/residue: 0.1365 time to fit residues: 74.8911 Evaluate side-chains 333 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 101 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 107 optimal weight: 0.0010 chunk 133 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN B 269 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102125 restraints weight = 31427.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100416 restraints weight = 28402.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101473 restraints weight = 28600.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101982 restraints weight = 20557.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102358 restraints weight = 18578.750| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18044 Z= 0.157 Angle : 0.609 11.340 24450 Z= 0.311 Chirality : 0.043 0.196 2966 Planarity : 0.004 0.050 3102 Dihedral : 5.466 58.927 2512 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 4.43 % Allowed : 20.54 % Favored : 75.03 % 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: -2.15 (0.17), residues: 2350 helix: -0.38 (0.17), residues: 993 sheet: -1.29 (0.31), residues: 292 loop : -2.51 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 82 TYR 0.015 0.001 TYR E 259 PHE 0.040 0.001 PHE C 37 TRP 0.012 0.001 TRP A 212 HIS 0.003 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (18044) covalent geometry : angle 0.60853 / 0.31 (24450) hydrogen bonds : bond 0.03733 / 2.47 ( 652) hydrogen bonds : angle 4.66449 / 3.21 ( 1878) *********************** 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 371 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 288 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 19 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8510 (pt) REVERT: B 73 ASP cc_start: 0.7498 (m-30) cc_final: 0.7224 (m-30) REVERT: C 19 ASN cc_start: 0.8560 (p0) cc_final: 0.8224 (p0) REVERT: C 84 GLN cc_start: 0.8179 (pp30) cc_final: 0.7750 (pp30) REVERT: D 24 MET cc_start: 0.9174 (ttp) cc_final: 0.8872 (ttm) REVERT: D 130 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 234 ARG cc_start: 0.6137 (ttt180) cc_final: 0.5331 (mtm-85) REVERT: E 246 LYS cc_start: 0.9157 (tttp) cc_final: 0.8491 (pttp) REVERT: F 18 GLU cc_start: 0.8007 (pm20) cc_final: 0.7544 (pm20) REVERT: F 78 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7797 (mtpt) REVERT: G 167 LEU cc_start: 0.7984 (tp) cc_final: 0.6965 (pt) REVERT: G 168 ASN cc_start: 0.8291 (m110) cc_final: 0.7948 (m-40) REVERT: G 170 LEU cc_start: 0.7797 (pt) cc_final: 0.7531 (mp) REVERT: H 45 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7279 (mm110) REVERT: H 134 MET cc_start: 0.6378 (mtt) cc_final: 0.5640 (ttp) REVERT: I 50 ASN cc_start: 0.8391 (m-40) cc_final: 0.7800 (m110) REVERT: I 134 MET cc_start: 0.6988 (mmt) cc_final: 0.6551 (mmm) REVERT: I 141 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: J 87 ASP cc_start: 0.6898 (m-30) cc_final: 0.6688 (p0) REVERT: J 189 ILE cc_start: 0.7758 (mm) cc_final: 0.7430 (tp) REVERT: J 192 PHE cc_start: 0.6038 (t80) cc_final: 0.5422 (t80) REVERT: K 7 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: L 70 SER cc_start: 0.5494 (OUTLIER) cc_final: 0.5034 (t) REVERT: L 134 MET cc_start: 0.6500 (tmm) cc_final: 0.5984 (tmm) REVERT: L 186 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6579 (pp20) outliers start: 83 outliers final: 64 residues processed: 349 average time/residue: 0.1375 time to fit residues: 73.5926 Evaluate side-chains 340 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 45 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** L 50 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 = 0.3706 r_free = 0.3706 target = 0.131930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099718 restraints weight = 31583.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099507 restraints weight = 26983.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100439 restraints weight = 24041.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100826 restraints weight = 18102.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101111 restraints weight = 17477.116| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18044 Z= 0.233 Angle : 0.671 11.814 24450 Z= 0.344 Chirality : 0.045 0.194 2966 Planarity : 0.004 0.054 3102 Dihedral : 5.688 59.336 2512 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 4.48 % Allowed : 21.08 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.17), residues: 2350 helix: -0.49 (0.16), residues: 1003 sheet: -1.44 (0.31), residues: 292 loop : -2.49 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 82 TYR 0.017 0.002 TYR E 29 PHE 0.015 0.002 PHE G 13 TRP 0.014 0.002 TRP A 212 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (18044) covalent geometry : angle 0.67119 / 0.34 (24450) hydrogen bonds : bond 0.04427 / 2.95 ( 652) hydrogen bonds : angle 4.97853 / 3.41 ( 1878) *********************** 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 367 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 283 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: B 19 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8610 (pt) REVERT: C 19 ASN cc_start: 0.8542 (p0) cc_final: 0.8268 (p0) REVERT: C 84 GLN cc_start: 0.8029 (pp30) cc_final: 0.7701 (pp30) REVERT: D 24 MET cc_start: 0.9163 (ttp) cc_final: 0.8860 (ttm) REVERT: D 130 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7896 (tm-30) REVERT: E 246 LYS cc_start: 0.9112 (tttp) cc_final: 0.8536 (pttp) REVERT: F 62 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7741 (tpt170) REVERT: F 90 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8272 (mm-30) REVERT: G 98 LEU cc_start: 0.7187 (mp) cc_final: 0.6781 (mt) REVERT: G 167 LEU cc_start: 0.8051 (tp) cc_final: 0.7047 (pt) REVERT: G 168 ASN cc_start: 0.8329 (m110) cc_final: 0.7972 (m-40) REVERT: H 45 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7280 (mm110) REVERT: H 96 GLU cc_start: 0.7130 (pm20) cc_final: 0.6884 (pm20) REVERT: H 134 MET cc_start: 0.6428 (mtt) cc_final: 0.5680 (ttp) REVERT: I 50 ASN cc_start: 0.8332 (m-40) cc_final: 0.7736 (m110) REVERT: J 189 ILE cc_start: 0.7747 (mm) cc_final: 0.7405 (tp) REVERT: K 7 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: L 134 MET cc_start: 0.6601 (tmm) cc_final: 0.6035 (tmm) REVERT: L 186 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6457 (pp20) outliers start: 84 outliers final: 68 residues processed: 345 average time/residue: 0.1351 time to fit residues: 71.6232 Evaluate side-chains 340 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN K 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103105 restraints weight = 31208.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101774 restraints weight = 25688.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102646 restraints weight = 26554.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103343 restraints weight = 18660.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103630 restraints weight = 16942.332| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18044 Z= 0.110 Angle : 0.592 12.959 24450 Z= 0.300 Chirality : 0.042 0.173 2966 Planarity : 0.003 0.047 3102 Dihedral : 5.373 60.140 2511 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.40 % Rotamer: Outliers : 3.52 % Allowed : 22.36 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.17), residues: 2350 helix: -0.05 (0.17), residues: 1003 sheet: -1.24 (0.32), residues: 292 loop : -2.42 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 82 TYR 0.014 0.001 TYR E 29 PHE 0.045 0.001 PHE C 37 TRP 0.007 0.001 TRP D 212 HIS 0.001 0.000 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (18044) covalent geometry : angle 0.59248 / 0.30 (24450) hydrogen bonds : bond 0.03112 / 2.06 ( 652) hydrogen bonds : angle 4.49555 / 3.07 ( 1878) *********************** 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 363 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8504 (pt) REVERT: B 73 ASP cc_start: 0.7442 (m-30) cc_final: 0.7212 (m-30) REVERT: C 19 ASN cc_start: 0.8508 (p0) cc_final: 0.8164 (p0) REVERT: D 24 MET cc_start: 0.9146 (ttp) cc_final: 0.8863 (ttm) REVERT: D 130 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 234 ARG cc_start: 0.6000 (ttt180) cc_final: 0.5505 (mtm-85) REVERT: E 246 LYS cc_start: 0.9123 (tttp) cc_final: 0.8485 (pttp) REVERT: F 18 GLU cc_start: 0.8122 (pm20) cc_final: 0.7831 (pm20) REVERT: F 62 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7714 (tpt170) REVERT: F 78 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7757 (mtpt) REVERT: F 90 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8233 (mm-30) REVERT: G 167 LEU cc_start: 0.8019 (tp) cc_final: 0.7010 (pt) REVERT: G 168 ASN cc_start: 0.8262 (m110) cc_final: 0.7949 (m-40) REVERT: H 45 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7176 (mm110) REVERT: H 134 MET cc_start: 0.6387 (mtt) cc_final: 0.5679 (ttp) REVERT: H 135 ASN cc_start: 0.7005 (p0) cc_final: 0.6740 (p0) REVERT: I 50 ASN cc_start: 0.8264 (m-40) cc_final: 0.7636 (m110) REVERT: I 134 MET cc_start: 0.6964 (mmt) cc_final: 0.6568 (mmm) REVERT: J 143 ASP cc_start: 0.8354 (m-30) cc_final: 0.7121 (t0) REVERT: J 189 ILE cc_start: 0.7668 (mm) cc_final: 0.7430 (tp) REVERT: L 70 SER cc_start: 0.5430 (OUTLIER) cc_final: 0.5116 (t) REVERT: L 134 MET cc_start: 0.6514 (tmm) cc_final: 0.5995 (tmm) REVERT: L 186 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6525 (pp20) outliers start: 66 outliers final: 53 residues processed: 347 average time/residue: 0.1348 time to fit residues: 71.9305 Evaluate side-chains 334 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 52 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 195 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 102 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105475 restraints weight = 31153.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104555 restraints weight = 24473.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105416 restraints weight = 28987.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105923 restraints weight = 18291.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106388 restraints weight = 16366.781| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18044 Z= 0.100 Angle : 0.594 13.223 24450 Z= 0.300 Chirality : 0.041 0.171 2966 Planarity : 0.003 0.057 3102 Dihedral : 5.115 61.745 2511 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 2.93 % Allowed : 23.43 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2350 helix: 0.28 (0.17), residues: 1002 sheet: -1.18 (0.31), residues: 297 loop : -2.34 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 82 TYR 0.013 0.001 TYR E 29 PHE 0.019 0.001 PHE H 13 TRP 0.006 0.001 TRP A 183 HIS 0.003 0.000 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (18044) covalent geometry : angle 0.59393 / 0.30 (24450) hydrogen bonds : bond 0.02751 / 1.82 ( 652) hydrogen bonds : angle 4.26767 / 2.92 ( 1878) *********************** 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 358 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8431 (tt0) cc_final: 0.8207 (tt0) REVERT: B 19 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8403 (pt) REVERT: C 19 ASN cc_start: 0.8490 (p0) cc_final: 0.8148 (p0) REVERT: D 24 MET cc_start: 0.9098 (ttp) cc_final: 0.8790 (ttm) REVERT: D 130 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7691 (tm-30) REVERT: D 187 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: D 234 ARG cc_start: 0.6087 (ttt180) cc_final: 0.5652 (mtm-85) REVERT: E 246 LYS cc_start: 0.9093 (tttp) cc_final: 0.8496 (pttp) REVERT: F 62 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7726 (tpt170) REVERT: F 78 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7754 (mtpt) REVERT: G 64 THR cc_start: 0.8222 (m) cc_final: 0.7997 (p) REVERT: G 167 LEU cc_start: 0.7998 (tp) cc_final: 0.6962 (pt) REVERT: G 168 ASN cc_start: 0.8235 (m110) cc_final: 0.7902 (m-40) REVERT: G 170 LEU cc_start: 0.7747 (pt) cc_final: 0.7417 (mp) REVERT: G 183 MET cc_start: 0.8169 (tpp) cc_final: 0.7850 (mmm) REVERT: H 13 PHE cc_start: 0.8033 (t80) cc_final: 0.7766 (t80) REVERT: H 45 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7180 (mm110) REVERT: H 100 GLU cc_start: 0.7636 (pp20) cc_final: 0.7151 (tp30) REVERT: H 134 MET cc_start: 0.6198 (mtt) cc_final: 0.5642 (ttp) REVERT: I 50 ASN cc_start: 0.8242 (m-40) cc_final: 0.7640 (m110) REVERT: I 60 MET cc_start: 0.8018 (tpp) cc_final: 0.7574 (ttm) REVERT: I 134 MET cc_start: 0.6984 (mmt) cc_final: 0.6759 (mmp) REVERT: I 141 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: J 143 ASP cc_start: 0.8209 (m-30) cc_final: 0.7060 (t0) REVERT: J 189 ILE cc_start: 0.7721 (mm) cc_final: 0.7439 (tp) REVERT: L 70 SER cc_start: 0.5252 (OUTLIER) cc_final: 0.4968 (t) REVERT: L 134 MET cc_start: 0.6471 (tmm) cc_final: 0.5965 (tmm) REVERT: L 156 GLU cc_start: 0.6870 (pm20) cc_final: 0.6664 (pm20) REVERT: L 186 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6624 (pp20) outliers start: 55 outliers final: 43 residues processed: 346 average time/residue: 0.1352 time to fit residues: 72.0328 Evaluate side-chains 318 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 259 TYR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU 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: 0.8980 chunk 28 optimal weight: 0.8980 chunk 204 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 111 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 198 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN K 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106387 restraints weight = 31237.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104387 restraints weight = 28385.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105655 restraints weight = 28622.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106020 restraints weight = 19927.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106360 restraints weight = 18709.141| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18044 Z= 0.100 Angle : 0.598 13.324 24450 Z= 0.298 Chirality : 0.041 0.168 2966 Planarity : 0.003 0.046 3102 Dihedral : 5.009 62.284 2511 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 2.67 % Allowed : 23.59 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2350 helix: 0.50 (0.17), residues: 1018 sheet: -1.15 (0.31), residues: 301 loop : -2.30 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 82 TYR 0.015 0.001 TYR E 29 PHE 0.047 0.001 PHE C 37 TRP 0.006 0.001 TRP D 183 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (18044) covalent geometry : angle 0.59828 / 0.30 (24450) hydrogen bonds : bond 0.02625 / 1.73 ( 652) hydrogen bonds : angle 4.15921 / 2.85 ( 1878) ********************** 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 340 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8426 (tt0) cc_final: 0.8102 (tt0) REVERT: B 19 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8424 (pt) REVERT: B 73 ASP cc_start: 0.7431 (m-30) cc_final: 0.7175 (m-30) REVERT: B 154 MET cc_start: 0.8551 (ptp) cc_final: 0.8345 (ptp) REVERT: C 19 ASN cc_start: 0.8519 (p0) cc_final: 0.8183 (p0) REVERT: D 130 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 187 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: D 234 ARG cc_start: 0.6119 (ttt180) cc_final: 0.5519 (mtm-85) REVERT: E 246 LYS cc_start: 0.9095 (tttp) cc_final: 0.8505 (pttp) REVERT: F 78 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7771 (mtpt) REVERT: G 167 LEU cc_start: 0.7958 (tp) cc_final: 0.6933 (pt) REVERT: G 168 ASN cc_start: 0.8227 (m110) cc_final: 0.7896 (m-40) REVERT: G 170 LEU cc_start: 0.7653 (pt) cc_final: 0.7344 (mp) REVERT: H 13 PHE cc_start: 0.8017 (t80) cc_final: 0.7495 (t80) REVERT: H 45 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7132 (mm110) REVERT: H 100 GLU cc_start: 0.7594 (pp20) cc_final: 0.7204 (tp30) REVERT: H 134 MET cc_start: 0.6186 (mtt) cc_final: 0.5549 (ttp) REVERT: I 50 ASN cc_start: 0.8216 (m-40) cc_final: 0.7618 (m110) REVERT: I 55 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6966 (mtm-85) REVERT: I 60 MET cc_start: 0.7979 (tpp) cc_final: 0.7600 (ttm) REVERT: I 134 MET cc_start: 0.6977 (mmt) cc_final: 0.6655 (mmp) REVERT: I 141 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: J 189 ILE cc_start: 0.7947 (mm) cc_final: 0.7690 (tp) REVERT: L 70 SER cc_start: 0.5184 (OUTLIER) cc_final: 0.4902 (t) REVERT: L 134 MET cc_start: 0.6493 (tmm) cc_final: 0.5987 (tmm) REVERT: L 156 GLU cc_start: 0.6861 (pm20) cc_final: 0.6462 (pm20) REVERT: L 186 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6575 (pp20) outliers start: 50 outliers final: 41 residues processed: 331 average time/residue: 0.1324 time to fit residues: 67.8014 Evaluate side-chains 319 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 259 TYR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 0.0870 chunk 226 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN B 180 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101973 restraints weight = 31499.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101693 restraints weight = 29216.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102481 restraints weight = 31490.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102665 restraints weight = 21798.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103160 restraints weight = 19310.046| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18044 Z= 0.177 Angle : 0.653 13.591 24450 Z= 0.330 Chirality : 0.044 0.179 2966 Planarity : 0.004 0.057 3102 Dihedral : 5.257 62.015 2511 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.57 % Favored : 92.38 % Rotamer: Outliers : 2.88 % Allowed : 23.75 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2350 helix: 0.26 (0.17), residues: 1008 sheet: -1.22 (0.31), residues: 294 loop : -2.20 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 82 TYR 0.016 0.001 TYR E 29 PHE 0.015 0.001 PHE G 13 TRP 0.013 0.002 TRP A 212 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (18044) covalent geometry : angle 0.65318 / 0.33 (24450) hydrogen bonds : bond 0.03854 / 2.57 ( 652) hydrogen bonds : angle 4.56679 / 3.13 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.89 seconds wall clock time: 52 minutes 22.31 seconds (3142.31 seconds total)