Starting phenix.real_space_refine on Thu Mar 5 00:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d09_30527/03_2026/7d09_30527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d09_30527/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d09_30527/03_2026/7d09_30527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d09_30527/03_2026/7d09_30527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d09_30527/03_2026/7d09_30527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d09_30527/03_2026/7d09_30527.map" } 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "E" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.25 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.59 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: 2.88 Time building geometry restraints manager: 2.36 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: 9531 17.65 - 35.31: 963 35.31 - 52.96: 240 52.96 - 70.61: 110 70.61 - 88.26: 30 Dihedral angle restraints: 10874 sinusoidal: 4132 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 10871 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 17.110 88.263 6546 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 covalent geometry : bond 0.00746 (18044) covalent geometry : angle 1.11181 (24450) hydrogen bonds : bond 0.30783 ( 652) hydrogen bonds : angle 10.82672 ( 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 : 0.670 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: 0.1510 time to fit residues: 117.0572 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 : 0.682 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 35 ASN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102695 restraints weight = 31509.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102536 restraints weight = 25043.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103206 restraints weight = 29882.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103496 restraints weight = 19651.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103924 restraints weight = 17565.351| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18044 Z= 0.146 Angle : 0.655 8.298 24450 Z= 0.344 Chirality : 0.043 0.177 2966 Planarity : 0.005 0.047 3102 Dihedral : 9.611 75.248 2663 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.55 % Rotamer: Outliers : 4.06 % Allowed : 15.42 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.14), residues: 2350 helix: -2.88 (0.12), residues: 997 sheet: -2.36 (0.27), residues: 300 loop : -3.06 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 140 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 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00326 (18044) covalent geometry : angle 0.65532 (24450) hydrogen bonds : bond 0.05039 ( 652) hydrogen bonds : angle 5.82102 ( 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 432 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 87 MET cc_start: 0.8005 (tmm) cc_final: 0.7672 (tmm) REVERT: A 116 GLU cc_start: 0.7567 (tt0) cc_final: 0.7357 (mt-10) REVERT: B 75 LYS cc_start: 0.7293 (tttm) cc_final: 0.7085 (tttm) REVERT: C 18 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: C 19 ASN cc_start: 0.8525 (p0) cc_final: 0.8095 (p0) REVERT: D 24 MET cc_start: 0.9179 (ttp) cc_final: 0.8798 (ttm) REVERT: D 116 GLU cc_start: 0.7412 (tt0) cc_final: 0.7023 (mt-10) REVERT: D 234 ARG cc_start: 0.5938 (ttt180) cc_final: 0.5430 (mtm-85) REVERT: E 246 LYS cc_start: 0.9095 (tttp) cc_final: 0.8398 (pttp) REVERT: F 18 GLU cc_start: 0.8194 (pm20) cc_final: 0.7931 (pm20) REVERT: F 84 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: G 27 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7735 (tppp) REVERT: G 99 LYS cc_start: 0.8166 (mppt) cc_final: 0.7907 (mptt) REVERT: H 96 GLU cc_start: 0.7525 (pm20) cc_final: 0.6570 (pm20) REVERT: H 143 ASP cc_start: 0.7819 (p0) cc_final: 0.7603 (p0) REVERT: I 50 ASN cc_start: 0.8223 (m-40) cc_final: 0.7514 (m110) REVERT: I 141 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: J 192 PHE cc_start: 0.6076 (t80) cc_final: 0.5465 (t80) REVERT: K 7 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: K 97 GLN cc_start: 0.6281 (tt0) cc_final: 0.5381 (mm110) REVERT: L 191 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.4905 (ptmm) outliers start: 76 outliers final: 33 residues processed: 402 average time/residue: 0.1470 time to fit residues: 88.8637 Evaluate side-chains 330 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 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 80 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 145 LEU 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 75 VAL Chi-restraints excluded: chain D residue 13 GLU 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 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 10 VAL 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 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 191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 229 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 170 optimal weight: 40.0000 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 93 HIS H 35 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102340 restraints weight = 31556.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102182 restraints weight = 25957.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102533 restraints weight = 26936.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104543 restraints weight = 19550.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104449 restraints weight = 15066.612| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18044 Z= 0.136 Angle : 0.619 9.788 24450 Z= 0.319 Chirality : 0.043 0.162 2966 Planarity : 0.004 0.051 3102 Dihedral : 7.627 67.341 2586 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.60 % Rotamer: Outliers : 3.52 % Allowed : 17.77 % Favored : 78.71 % 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: -3.43 (0.15), residues: 2350 helix: -1.75 (0.15), residues: 1021 sheet: -1.86 (0.29), residues: 297 loop : -2.91 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 82 TYR 0.021 0.001 TYR E 259 PHE 0.011 0.001 PHE J 13 TRP 0.014 0.001 TRP A 212 HIS 0.002 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00307 (18044) covalent geometry : angle 0.61874 (24450) hydrogen bonds : bond 0.04082 ( 652) hydrogen bonds : angle 5.17985 ( 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 382 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 316 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: A 95 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: A 116 GLU cc_start: 0.7621 (tt0) cc_final: 0.7411 (mt-10) REVERT: C 19 ASN cc_start: 0.8463 (p0) cc_final: 0.8137 (p0) REVERT: C 91 ASP cc_start: 0.8239 (t0) cc_final: 0.7795 (t0) REVERT: D 24 MET cc_start: 0.9191 (ttp) cc_final: 0.8782 (ttm) REVERT: D 116 GLU cc_start: 0.7455 (tt0) cc_final: 0.7135 (mt-10) REVERT: D 130 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 230 THR cc_start: 0.9258 (t) cc_final: 0.8985 (m) REVERT: D 234 ARG cc_start: 0.6161 (ttt180) cc_final: 0.5585 (mtm-85) REVERT: E 75 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8387 (mmtm) REVERT: E 246 LYS cc_start: 0.9141 (tttp) cc_final: 0.8399 (pttp) REVERT: F 84 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: G 27 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7674 (mmmm) REVERT: G 99 LYS cc_start: 0.8159 (mppt) cc_final: 0.7880 (mptt) REVERT: G 167 LEU cc_start: 0.8025 (tp) cc_final: 0.6967 (pt) REVERT: G 168 ASN cc_start: 0.8336 (m110) cc_final: 0.7958 (m-40) REVERT: H 134 MET cc_start: 0.6248 (mtt) cc_final: 0.5971 (ttt) REVERT: H 143 ASP cc_start: 0.7759 (p0) cc_final: 0.7543 (p0) REVERT: I 50 ASN cc_start: 0.8250 (m-40) cc_final: 0.7597 (m110) REVERT: I 154 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7734 (mp) REVERT: J 192 PHE cc_start: 0.6070 (t80) cc_final: 0.5518 (t80) REVERT: K 7 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: K 97 GLN cc_start: 0.5673 (tt0) cc_final: 0.4911 (mm110) REVERT: L 186 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: L 191 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4770 (ptmm) outliers start: 66 outliers final: 44 residues processed: 359 average time/residue: 0.1470 time to fit residues: 78.9206 Evaluate side-chains 337 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 151 SER Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 263 HIS 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 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 E residue 271 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 GLN 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 35 ASN Chi-restraints excluded: chain H residue 154 LEU 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 185 LEU Chi-restraints excluded: chain L residue 7 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: 7.9990 chunk 163 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN K 35 ASN ** 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 = 0.3765 r_free = 0.3765 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103129 restraints weight = 31573.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101688 restraints weight = 25774.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102696 restraints weight = 26639.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103197 restraints weight = 18833.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103653 restraints weight = 17210.008| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18044 Z= 0.117 Angle : 0.592 9.406 24450 Z= 0.303 Chirality : 0.042 0.142 2966 Planarity : 0.003 0.043 3102 Dihedral : 7.060 68.754 2581 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 3.63 % Allowed : 18.62 % Favored : 77.75 % 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: -2.77 (0.16), residues: 2350 helix: -1.04 (0.16), residues: 1015 sheet: -1.59 (0.30), residues: 297 loop : -2.73 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 82 TYR 0.018 0.001 TYR E 259 PHE 0.038 0.001 PHE C 37 TRP 0.011 0.001 TRP A 212 HIS 0.001 0.000 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00261 (18044) covalent geometry : angle 0.59205 (24450) hydrogen bonds : bond 0.03484 ( 652) hydrogen bonds : angle 4.79336 ( 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 385 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.700 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: 0.8412 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: A 95 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: A 198 ASN cc_start: 0.8515 (m-40) cc_final: 0.8272 (m-40) REVERT: B 73 ASP cc_start: 0.7361 (m-30) cc_final: 0.7089 (m-30) REVERT: C 19 ASN cc_start: 0.8558 (p0) cc_final: 0.8190 (p0) REVERT: C 91 ASP cc_start: 0.8445 (t0) cc_final: 0.8061 (t0) REVERT: D 24 MET cc_start: 0.9158 (ttp) cc_final: 0.8774 (ttm) REVERT: D 116 GLU cc_start: 0.7467 (tt0) cc_final: 0.7235 (mt-10) REVERT: D 130 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 230 THR cc_start: 0.9232 (t) cc_final: 0.8942 (m) REVERT: D 234 ARG cc_start: 0.6101 (ttt180) cc_final: 0.5551 (mtm-85) REVERT: E 246 LYS cc_start: 0.9141 (tttp) cc_final: 0.8437 (pttp) REVERT: F 62 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7764 (mmm160) REVERT: F 79 MET cc_start: 0.8130 (mmp) cc_final: 0.7927 (mmm) REVERT: G 99 LYS cc_start: 0.8096 (mppt) cc_final: 0.7730 (mptt) REVERT: G 167 LEU cc_start: 0.7983 (tp) cc_final: 0.6991 (pt) REVERT: G 168 ASN cc_start: 0.8326 (m110) cc_final: 0.7874 (m-40) REVERT: H 45 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7411 (mm110) REVERT: H 134 MET cc_start: 0.6392 (mtt) cc_final: 0.5903 (ttt) REVERT: I 50 ASN cc_start: 0.8258 (m-40) cc_final: 0.7692 (m110) REVERT: J 143 ASP cc_start: 0.8180 (m-30) cc_final: 0.7003 (t0) REVERT: J 147 MET cc_start: 0.7226 (ptp) cc_final: 0.6916 (ptp) REVERT: J 192 PHE cc_start: 0.5999 (t80) cc_final: 0.5447 (t80) REVERT: K 97 GLN cc_start: 0.5874 (tt0) cc_final: 0.5106 (mm110) REVERT: L 70 SER cc_start: 0.5218 (OUTLIER) cc_final: 0.4623 (t) REVERT: L 191 LYS cc_start: 0.5099 (OUTLIER) cc_final: 0.4730 (ptmm) outliers start: 68 outliers final: 48 residues processed: 363 average time/residue: 0.1363 time to fit residues: 75.7847 Evaluate side-chains 337 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 95 GLU Chi-restraints excluded: chain A residue 203 SER 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 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 C residue 75 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 74 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 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 263 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 41 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 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H 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 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 153 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 7 GLU 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 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: 5.9990 chunk 17 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 185 optimal weight: 0.0070 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 overall best weight: 1.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104086 restraints weight = 31288.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103033 restraints weight = 25122.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103689 restraints weight = 26307.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104340 restraints weight = 19103.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104566 restraints weight = 17042.687| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3668 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= 0.101 Angle : 0.565 10.329 24450 Z= 0.290 Chirality : 0.041 0.188 2966 Planarity : 0.003 0.051 3102 Dihedral : 6.746 69.234 2580 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 3.84 % Allowed : 19.16 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.16), residues: 2350 helix: -0.51 (0.16), residues: 1002 sheet: -1.27 (0.31), residues: 289 loop : -2.61 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 82 TYR 0.016 0.001 TYR E 259 PHE 0.017 0.001 PHE H 13 TRP 0.009 0.001 TRP A 212 HIS 0.001 0.000 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00222 (18044) covalent geometry : angle 0.56535 (24450) hydrogen bonds : bond 0.03119 ( 652) hydrogen bonds : angle 4.52078 ( 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 375 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: A 198 ASN cc_start: 0.8457 (m-40) cc_final: 0.8238 (m-40) REVERT: C 19 ASN cc_start: 0.8580 (p0) cc_final: 0.8228 (p0) REVERT: C 54 LEU cc_start: 0.8504 (tp) cc_final: 0.8297 (tt) REVERT: D 24 MET cc_start: 0.9129 (ttp) cc_final: 0.8795 (ttm) REVERT: D 116 GLU cc_start: 0.7561 (tt0) cc_final: 0.7286 (mt-10) REVERT: D 130 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 234 ARG cc_start: 0.5892 (ttt180) cc_final: 0.5546 (mtm-85) REVERT: E 246 LYS cc_start: 0.9146 (tttp) cc_final: 0.8424 (pttp) REVERT: F 18 GLU cc_start: 0.7842 (pm20) cc_final: 0.7436 (pm20) REVERT: F 62 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7772 (mmm160) REVERT: F 78 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7770 (mtpt) REVERT: G 167 LEU cc_start: 0.8000 (tp) cc_final: 0.6989 (pt) REVERT: G 168 ASN cc_start: 0.8214 (m110) cc_final: 0.7854 (m-40) REVERT: H 13 PHE cc_start: 0.8093 (t80) cc_final: 0.7729 (t80) REVERT: H 45 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7270 (mm110) REVERT: H 97 GLN cc_start: 0.7211 (mp10) cc_final: 0.6792 (mt0) REVERT: H 134 MET cc_start: 0.6429 (mtt) cc_final: 0.5619 (ttp) REVERT: I 50 ASN cc_start: 0.8241 (m-40) cc_final: 0.7670 (m110) REVERT: J 143 ASP cc_start: 0.8080 (m-30) cc_final: 0.7002 (t0) REVERT: J 189 ILE cc_start: 0.7809 (mm) cc_final: 0.7588 (tp) REVERT: J 192 PHE cc_start: 0.5918 (t80) cc_final: 0.5388 (t80) REVERT: K 97 GLN cc_start: 0.5856 (tt0) cc_final: 0.5142 (mm110) REVERT: L 70 SER cc_start: 0.5297 (OUTLIER) cc_final: 0.4859 (t) REVERT: L 186 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: L 191 LYS cc_start: 0.5258 (OUTLIER) cc_final: 0.4890 (ptmm) outliers start: 72 outliers final: 57 residues processed: 354 average time/residue: 0.1379 time to fit residues: 74.9587 Evaluate side-chains 337 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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 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 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 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 172 MET Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL 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 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 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 162 VAL 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 170 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 191 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN B 269 ASN C 89 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103897 restraints weight = 31381.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103311 restraints weight = 28420.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104309 restraints weight = 30887.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104494 restraints weight = 20685.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105041 restraints weight = 18709.011| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18044 Z= 0.126 Angle : 0.595 10.905 24450 Z= 0.301 Chirality : 0.042 0.192 2966 Planarity : 0.003 0.049 3102 Dihedral : 6.620 69.721 2578 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 4.38 % Allowed : 19.48 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.17), residues: 2350 helix: -0.21 (0.17), residues: 987 sheet: -1.19 (0.31), residues: 290 loop : -2.48 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 82 TYR 0.014 0.001 TYR E 259 PHE 0.039 0.001 PHE C 37 TRP 0.011 0.001 TRP A 212 HIS 0.002 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00291 (18044) covalent geometry : angle 0.59513 (24450) hydrogen bonds : bond 0.03335 ( 652) hydrogen bonds : angle 4.51119 ( 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 373 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 198 ASN cc_start: 0.8442 (m-40) cc_final: 0.8221 (m-40) REVERT: B 19 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8504 (pt) REVERT: B 73 ASP cc_start: 0.7501 (m-30) cc_final: 0.7231 (m-30) REVERT: C 19 ASN cc_start: 0.8524 (p0) cc_final: 0.8207 (p0) REVERT: D 24 MET cc_start: 0.9148 (ttp) cc_final: 0.8825 (ttm) REVERT: D 72 TYR cc_start: 0.8724 (t80) cc_final: 0.8416 (t80) REVERT: D 130 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 234 ARG cc_start: 0.6008 (ttt180) cc_final: 0.5491 (mtm-85) REVERT: E 246 LYS cc_start: 0.9094 (tttp) cc_final: 0.8462 (pttp) REVERT: F 18 GLU cc_start: 0.7847 (pm20) cc_final: 0.7534 (pm20) REVERT: F 62 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7667 (mmm160) REVERT: F 78 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7794 (mtpt) REVERT: G 167 LEU cc_start: 0.7875 (tp) cc_final: 0.6883 (pt) REVERT: G 168 ASN cc_start: 0.8203 (m110) cc_final: 0.7885 (m-40) REVERT: G 170 LEU cc_start: 0.7775 (pt) cc_final: 0.7498 (mp) REVERT: G 188 LEU cc_start: 0.8945 (mt) cc_final: 0.8739 (mt) REVERT: H 45 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7273 (mm110) REVERT: H 134 MET cc_start: 0.6238 (mtt) cc_final: 0.5557 (ttp) REVERT: I 50 ASN cc_start: 0.8273 (m-40) cc_final: 0.7675 (m110) REVERT: I 134 MET cc_start: 0.6950 (mmt) cc_final: 0.6547 (mmm) REVERT: J 189 ILE cc_start: 0.7825 (mm) cc_final: 0.7604 (tp) REVERT: J 192 PHE cc_start: 0.5954 (t80) cc_final: 0.5408 (t80) REVERT: K 7 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: L 70 SER cc_start: 0.5274 (OUTLIER) cc_final: 0.4811 (t) REVERT: L 156 GLU cc_start: 0.6692 (pm20) cc_final: 0.6360 (pm20) REVERT: L 186 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6507 (pp20) REVERT: L 191 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4843 (ptmm) outliers start: 82 outliers final: 61 residues processed: 350 average time/residue: 0.1334 time to fit residues: 71.6881 Evaluate side-chains 335 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 155 ASN 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 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 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 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 172 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 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL 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 76 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 26 MET 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 150 THR Chi-restraints excluded: chain K residue 162 VAL 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 Chi-restraints excluded: chain L residue 191 LYS 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: 7.9990 chunk 158 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 137 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN K 180 GLN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101595 restraints weight = 31533.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100148 restraints weight = 27979.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101082 restraints weight = 27814.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101548 restraints weight = 20311.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101826 restraints weight = 18553.680| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3806 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= 0.174 Angle : 0.624 12.165 24450 Z= 0.317 Chirality : 0.044 0.187 2966 Planarity : 0.004 0.054 3102 Dihedral : 6.765 72.205 2578 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 4.43 % Allowed : 19.69 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 2350 helix: -0.17 (0.17), residues: 991 sheet: -1.29 (0.31), residues: 292 loop : -2.44 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 82 TYR 0.013 0.001 TYR E 29 PHE 0.015 0.001 PHE G 13 TRP 0.014 0.001 TRP A 212 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00412 (18044) covalent geometry : angle 0.62369 (24450) hydrogen bonds : bond 0.03860 ( 652) hydrogen bonds : angle 4.68642 ( 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 358 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 275 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 95 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: B 19 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8592 (pt) REVERT: C 19 ASN cc_start: 0.8573 (p0) cc_final: 0.8251 (p0) REVERT: D 24 MET cc_start: 0.9163 (ttp) cc_final: 0.8885 (ttm) REVERT: D 130 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 234 ARG cc_start: 0.6308 (ttt180) cc_final: 0.5530 (mtm-85) REVERT: E 246 LYS cc_start: 0.9130 (tttp) cc_final: 0.8491 (pttp) REVERT: G 27 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7888 (mmmt) REVERT: G 167 LEU cc_start: 0.7979 (tp) cc_final: 0.6918 (pt) REVERT: G 168 ASN cc_start: 0.8260 (m110) cc_final: 0.7935 (m-40) REVERT: G 170 LEU cc_start: 0.7808 (pt) cc_final: 0.7559 (mp) REVERT: H 45 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7262 (mm110) REVERT: H 134 MET cc_start: 0.6444 (mtt) cc_final: 0.5721 (ttt) REVERT: I 50 ASN cc_start: 0.8314 (m-40) cc_final: 0.7695 (m110) REVERT: I 134 MET cc_start: 0.6989 (mmt) cc_final: 0.6613 (mmm) REVERT: J 189 ILE cc_start: 0.7824 (mm) cc_final: 0.7582 (tp) REVERT: J 192 PHE cc_start: 0.6054 (t80) cc_final: 0.5459 (t80) REVERT: K 7 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: K 37 SER cc_start: 0.7397 (m) cc_final: 0.7121 (t) REVERT: L 134 MET cc_start: 0.6580 (tmm) cc_final: 0.6034 (tmm) REVERT: L 186 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6528 (pp20) outliers start: 83 outliers final: 64 residues processed: 335 average time/residue: 0.1321 time to fit residues: 67.9661 Evaluate side-chains 331 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 262 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 76 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 104 ASP 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 155 ASN 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 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 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 D residue 230 THR Chi-restraints excluded: chain E residue 28 ILE 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 172 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 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 91 THR 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 I residue 182 THR Chi-restraints excluded: chain J residue 26 MET 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 150 THR Chi-restraints excluded: chain K residue 162 VAL 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: 1.9990 chunk 135 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 187 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN K 97 GLN K 180 GLN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102180 restraints weight = 31287.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100539 restraints weight = 28411.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101583 restraints weight = 27970.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102015 restraints weight = 20286.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102284 restraints weight = 18631.542| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3909 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= 0.145 Angle : 0.616 13.019 24450 Z= 0.311 Chirality : 0.043 0.181 2966 Planarity : 0.003 0.051 3102 Dihedral : 6.589 74.375 2573 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.15 % Favored : 92.81 % Rotamer: Outliers : 4.32 % Allowed : 19.90 % Favored : 75.77 % 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: -1.84 (0.17), residues: 2350 helix: -0.03 (0.17), residues: 1000 sheet: -1.29 (0.31), residues: 292 loop : -2.41 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 82 TYR 0.011 0.001 TYR G 169 PHE 0.044 0.001 PHE C 37 TRP 0.011 0.001 TRP A 212 HIS 0.002 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00339 (18044) covalent geometry : angle 0.61581 (24450) hydrogen bonds : bond 0.03577 ( 652) hydrogen bonds : angle 4.58721 ( 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 359 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 278 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8577 (pt) REVERT: B 73 ASP cc_start: 0.7464 (m-30) cc_final: 0.7221 (m-30) REVERT: C 19 ASN cc_start: 0.8517 (p0) cc_final: 0.8195 (p0) REVERT: D 24 MET cc_start: 0.9155 (ttp) cc_final: 0.8845 (ttm) REVERT: D 130 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 234 ARG cc_start: 0.6227 (ttt180) cc_final: 0.5494 (mtm-85) REVERT: E 246 LYS cc_start: 0.9133 (tttp) cc_final: 0.8502 (pttp) REVERT: G 27 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7872 (mmmm) REVERT: G 167 LEU cc_start: 0.7993 (tp) cc_final: 0.6934 (pt) REVERT: G 168 ASN cc_start: 0.8297 (m110) cc_final: 0.7928 (m-40) REVERT: G 170 LEU cc_start: 0.7791 (pt) cc_final: 0.7564 (mp) REVERT: H 45 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7221 (mm110) REVERT: H 134 MET cc_start: 0.6425 (mtt) cc_final: 0.5722 (ttt) REVERT: I 50 ASN cc_start: 0.8300 (m-40) cc_final: 0.7679 (m110) REVERT: I 134 MET cc_start: 0.7068 (mmt) cc_final: 0.6682 (mmm) REVERT: I 141 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: J 189 ILE cc_start: 0.7774 (mm) cc_final: 0.7525 (tp) REVERT: J 192 PHE cc_start: 0.6046 (t80) cc_final: 0.5415 (t80) REVERT: K 7 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: K 37 SER cc_start: 0.7537 (m) cc_final: 0.7220 (t) REVERT: L 70 SER cc_start: 0.5394 (OUTLIER) cc_final: 0.4922 (t) REVERT: L 134 MET cc_start: 0.6560 (tmm) cc_final: 0.6037 (tmm) REVERT: L 186 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6631 (pp20) outliers start: 81 outliers final: 64 residues processed: 337 average time/residue: 0.1323 time to fit residues: 68.4710 Evaluate side-chains 340 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 76 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 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 155 ASN 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 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 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 D residue 230 THR Chi-restraints excluded: chain E residue 28 ILE 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 172 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 233 THR Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL 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 31 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 90 LEU 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 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: 0.5980 chunk 126 optimal weight: 1.9990 chunk 195 optimal weight: 0.0670 chunk 75 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 50.0000 chunk 121 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104890 restraints weight = 31239.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103803 restraints weight = 26221.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104552 restraints weight = 28544.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105073 restraints weight = 19811.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105330 restraints weight = 18096.773| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4136 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= 0.103 Angle : 0.596 13.639 24450 Z= 0.299 Chirality : 0.042 0.174 2966 Planarity : 0.003 0.055 3102 Dihedral : 6.343 74.821 2573 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 3.26 % Allowed : 20.92 % Favored : 75.83 % 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: -1.61 (0.17), residues: 2350 helix: 0.24 (0.17), residues: 1007 sheet: -1.16 (0.31), residues: 292 loop : -2.39 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 82 TYR 0.012 0.001 TYR B 108 PHE 0.012 0.001 PHE G 22 TRP 0.006 0.001 TRP D 212 HIS 0.002 0.000 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00230 (18044) covalent geometry : angle 0.59581 (24450) hydrogen bonds : bond 0.02884 ( 652) hydrogen bonds : angle 4.31781 ( 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 360 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8422 (pt) REVERT: C 19 ASN cc_start: 0.8472 (p0) cc_final: 0.8125 (p0) REVERT: D 24 MET cc_start: 0.9106 (ttp) cc_final: 0.8791 (ttm) REVERT: D 72 TYR cc_start: 0.8731 (t80) cc_final: 0.8524 (t80) REVERT: D 130 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 187 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: D 234 ARG cc_start: 0.6137 (ttt180) cc_final: 0.5525 (mtm-85) REVERT: E 246 LYS cc_start: 0.9120 (tttp) cc_final: 0.8503 (pttp) REVERT: F 62 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7804 (mmt90) REVERT: F 78 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7622 (mtpt) REVERT: G 27 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7894 (mmmm) REVERT: G 167 LEU cc_start: 0.7892 (tp) cc_final: 0.6889 (pt) REVERT: G 168 ASN cc_start: 0.8216 (m110) cc_final: 0.7853 (m-40) REVERT: H 45 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7181 (mm110) REVERT: H 134 MET cc_start: 0.6281 (mtt) cc_final: 0.5561 (ttp) REVERT: I 50 ASN cc_start: 0.8258 (m-40) cc_final: 0.7664 (m110) REVERT: I 134 MET cc_start: 0.7092 (mmt) cc_final: 0.6767 (mmm) REVERT: I 141 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: J 189 ILE cc_start: 0.7694 (mm) cc_final: 0.7462 (tp) REVERT: J 192 PHE cc_start: 0.5914 (t80) cc_final: 0.5260 (t80) REVERT: K 7 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: L 70 SER cc_start: 0.5190 (OUTLIER) cc_final: 0.4834 (t) REVERT: L 134 MET cc_start: 0.6538 (tmm) cc_final: 0.6011 (tmm) REVERT: L 186 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6603 (pp20) outliers start: 61 outliers final: 49 residues processed: 342 average time/residue: 0.1357 time to fit residues: 70.4270 Evaluate side-chains 328 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 151 SER 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 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 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 177 PHE 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 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL 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 182 THR Chi-restraints excluded: chain J residue 90 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 163 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105127 restraints weight = 31264.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104615 restraints weight = 28345.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105416 restraints weight = 31959.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105774 restraints weight = 20957.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106290 restraints weight = 18878.976| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4252 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= 0.110 Angle : 0.606 14.190 24450 Z= 0.303 Chirality : 0.042 0.172 2966 Planarity : 0.003 0.050 3102 Dihedral : 6.284 74.010 2573 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.02 % Rotamer: Outliers : 3.15 % Allowed : 21.24 % Favored : 75.61 % 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: -1.45 (0.17), residues: 2350 helix: 0.43 (0.17), residues: 1011 sheet: -1.13 (0.31), residues: 294 loop : -2.36 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 82 TYR 0.011 0.001 TYR I 145 PHE 0.046 0.001 PHE C 37 TRP 0.007 0.001 TRP D 212 HIS 0.001 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00254 (18044) covalent geometry : angle 0.60607 (24450) hydrogen bonds : bond 0.02907 ( 652) hydrogen bonds : angle 4.26842 ( 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 344 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.8211 (m-40) cc_final: 0.7997 (m110) REVERT: B 19 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8432 (pt) REVERT: B 73 ASP cc_start: 0.7396 (m-30) cc_final: 0.7119 (m-30) REVERT: B 271 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5808 (m) REVERT: C 19 ASN cc_start: 0.8445 (p0) cc_final: 0.8121 (p0) REVERT: D 24 MET cc_start: 0.9121 (ttp) cc_final: 0.8817 (ttm) REVERT: D 95 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: D 130 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7740 (tm-30) REVERT: D 187 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: D 234 ARG cc_start: 0.6069 (ttt180) cc_final: 0.5591 (mtm-85) REVERT: E 246 LYS cc_start: 0.9097 (tttp) cc_final: 0.8484 (pttp) REVERT: F 62 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7735 (mmt90) REVERT: F 78 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7656 (mtpt) REVERT: G 27 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7913 (mmmm) REVERT: G 167 LEU cc_start: 0.7928 (tp) cc_final: 0.7003 (pt) REVERT: G 168 ASN cc_start: 0.8114 (m110) cc_final: 0.7853 (m-40) REVERT: H 13 PHE cc_start: 0.8037 (t80) cc_final: 0.7764 (t80) REVERT: H 45 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7198 (mm110) REVERT: H 134 MET cc_start: 0.6242 (mtt) cc_final: 0.5542 (ttp) REVERT: I 50 ASN cc_start: 0.8261 (m-40) cc_final: 0.7674 (m110) REVERT: I 134 MET cc_start: 0.7087 (mmt) cc_final: 0.6757 (mmm) REVERT: I 141 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: J 134 MET cc_start: 0.7420 (ppp) cc_final: 0.6935 (ppp) REVERT: J 189 ILE cc_start: 0.7927 (mm) cc_final: 0.7707 (tp) REVERT: J 192 PHE cc_start: 0.5869 (t80) cc_final: 0.5229 (t80) REVERT: K 7 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: L 70 SER cc_start: 0.5151 (OUTLIER) cc_final: 0.4804 (t) REVERT: L 134 MET cc_start: 0.6566 (tmm) cc_final: 0.6033 (tmm) REVERT: L 186 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6558 (pp20) outliers start: 59 outliers final: 51 residues processed: 329 average time/residue: 0.1392 time to fit residues: 69.6314 Evaluate side-chains 330 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 95 GLU 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 151 SER 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 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 13 GLU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 172 MET 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 6 ASN Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain G residue 93 PHE 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 90 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 0.0770 chunk 226 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 118 optimal weight: 0.0010 chunk 175 optimal weight: 9.9990 overall best weight: 2.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN H 35 ASN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103930 restraints weight = 31451.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103409 restraints weight = 28640.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104472 restraints weight = 25242.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104931 restraints weight = 18989.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105304 restraints weight = 18195.093| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18044 Z= 0.132 Angle : 0.620 14.288 24450 Z= 0.311 Chirality : 0.043 0.208 2966 Planarity : 0.004 0.055 3102 Dihedral : 6.267 74.722 2573 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.94 % Rotamer: Outliers : 3.47 % Allowed : 21.18 % Favored : 75.35 % 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: -1.38 (0.17), residues: 2350 helix: 0.46 (0.17), residues: 1003 sheet: -1.12 (0.31), residues: 294 loop : -2.27 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 82 TYR 0.013 0.001 TYR D 72 PHE 0.017 0.001 PHE H 13 TRP 0.009 0.001 TRP A 212 HIS 0.003 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00309 (18044) covalent geometry : angle 0.61972 (24450) hydrogen bonds : bond 0.03246 ( 652) hydrogen bonds : angle 4.35879 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2863.56 seconds wall clock time: 50 minutes 23.34 seconds (3023.34 seconds total)