Starting phenix.real_space_refine on Sun Aug 24 06:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0a_30528/08_2025/7d0a_30528.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 S 88 5.16 5 C 11342 2.51 5 N 2988 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17804 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.91, per 1000 atoms: 0.22 Number of scatterers: 17804 At special positions: 0 Unit cell: (134.788, 126.092, 153.267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 88 16.00 P 4 15.00 O 3380 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: 1.28 Conformation dependent library (CDL) restraints added in 552.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 87 helices and 16 sheets defined 46.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.754A pdb=" N GLU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.711A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 76 removed outlier: 4.657A pdb=" N LEU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.695A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.941A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.784A pdb=" N MET A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.663A pdb=" N ALA A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.838A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.581A pdb=" N MET A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 220 removed outlier: 3.676A pdb=" N ASP A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A 198 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.724A pdb=" N THR A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.639A pdb=" N LEU A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.593A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.018A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.620A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.681A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.522A pdb=" N SER B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.535A pdb=" N GLN B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.723A pdb=" N ALA C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 removed outlier: 4.315A pdb=" N VAL C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.606A pdb=" N GLN C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'D' and resid 2 through 30 removed outlier: 3.931A pdb=" N GLN D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.712A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 76 removed outlier: 4.658A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.696A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 removed outlier: 3.942A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.784A pdb=" N MET D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.663A pdb=" N ALA D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 175 removed outlier: 3.838A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.581A pdb=" N MET D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 220 removed outlier: 3.676A pdb=" N ASP D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN D 198 " --> pdb=" O HIS D 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS D 210 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.724A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.640A pdb=" N LEU D 250 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.593A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 122 through 136 removed outlier: 4.018A pdb=" N LEU E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.620A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.683A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.522A pdb=" N SER E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.537A pdb=" N GLN E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 4.296A pdb=" N THR E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.723A pdb=" N ALA F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.316A pdb=" N VAL F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 removed outlier: 3.606A pdb=" N GLN F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'G' and resid 10 through 26 removed outlier: 3.813A pdb=" N ILE G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.774A pdb=" N LYS G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 135 removed outlier: 4.972A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 193 removed outlier: 3.757A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 30 removed outlier: 4.089A pdb=" N GLY H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL H 14 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 21 " --> pdb=" O PHE H 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 removed outlier: 3.532A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 removed outlier: 3.757A pdb=" N GLU H 108 " --> pdb=" O ASN H 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.041A pdb=" N THR H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 131 removed outlier: 3.984A pdb=" N GLN H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 191 Processing helix chain 'I' and resid 4 through 27 removed outlier: 3.786A pdb=" N GLY I 18 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 94 through 110 removed outlier: 4.309A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 133 removed outlier: 3.600A pdb=" N GLN I 129 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.876A pdb=" N LEU I 153 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU I 154 " --> pdb=" O ASN I 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 150 through 154' Processing helix chain 'I' and resid 184 through 191 Processing helix chain 'J' and resid 5 through 10 Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.720A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 110 removed outlier: 3.611A pdb=" N LYS J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 115 Processing helix chain 'J' and resid 127 through 135 removed outlier: 3.721A pdb=" N MET J 134 " --> pdb=" O LEU J 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN J 135 " --> pdb=" O ILE J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 193 removed outlier: 4.095A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 29 removed outlier: 4.029A pdb=" N LEU K 8 " --> pdb=" O ARG K 4 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE K 17 " --> pdb=" O PHE K 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET K 26 " --> pdb=" O PHE K 22 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 27 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 109 removed outlier: 3.594A pdb=" N LYS K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.986A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 191 removed outlier: 3.871A pdb=" N LEU K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 28 Processing helix chain 'L' and resid 94 through 109 removed outlier: 3.507A pdb=" N ASN L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 124 through 135 removed outlier: 3.739A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN L 133 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET L 134 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN L 135 " --> pdb=" O ILE L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 193 removed outlier: 3.670A pdb=" N LEU L 188 " --> pdb=" O ASP L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.624A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.508A pdb=" N THR B 42 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY B 93 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP B 174 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 222 through 223 removed outlier: 6.382A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.623A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 92 through 94 removed outlier: 6.041A pdb=" N GLY E 93 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP E 174 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 219 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 43 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 221 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL E 223 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'G' and resid 175 through 176 removed outlier: 8.188A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS G 57 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE G 161 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR G 59 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL G 162 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR G 145 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 40 through 43 removed outlier: 3.718A pdb=" N TYR H 40 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP H 85 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL H 68 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS H 57 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 175 through 176 removed outlier: 6.946A pdb=" N LYS I 43 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA I 44 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 82 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS I 57 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE I 161 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR I 59 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE I 146 " --> pdb=" O GLN I 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 41 through 46 removed outlier: 3.586A pdb=" N ALA J 80 " --> pdb=" O PHE J 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE J 146 " --> pdb=" O GLN J 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 137 through 141 removed outlier: 6.204A pdb=" N ILE J 140 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 70 through 73 removed outlier: 9.260A pdb=" N ILE K 176 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS K 43 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 64 through 66 removed outlier: 6.242A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 137 through 141 removed outlier: 3.654A pdb=" N THR K 138 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU K 170 " --> pdb=" O THR K 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 42 through 46 removed outlier: 3.575A pdb=" N PHE L 84 " --> pdb=" O MET L 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 79 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 70 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS L 57 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE L 161 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR L 59 " --> pdb=" O ILE L 161 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1998 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: 2.91 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 8 1.16 - 1.32: 3140 1.32 - 1.49: 6849 1.49 - 1.65: 7879 1.65 - 1.82: 168 Bond restraints: 18044 Sorted by residual: bond pdb=" O2 VO4 E 302 " pdb=" V VO4 E 302 " ideal model delta sigma weight residual 1.910 0.992 0.918 2.00e-02 2.50e+03 2.11e+03 bond pdb=" O2 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.992 0.918 2.00e-02 2.50e+03 2.11e+03 bond pdb=" O1 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.995 0.915 2.00e-02 2.50e+03 2.09e+03 bond pdb=" O3 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.995 0.915 2.00e-02 2.50e+03 2.09e+03 bond pdb=" O3 VO4 E 302 " pdb=" V VO4 E 302 " ideal model delta sigma weight residual 1.910 0.996 0.914 2.00e-02 2.50e+03 2.09e+03 ... (remaining 18039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.90: 24436 13.90 - 27.81: 8 27.81 - 41.71: 0 41.71 - 55.62: 0 55.62 - 69.52: 4 Bond angle restraints: 24448 Sorted by residual: angle pdb=" O1 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O4 VO4 E 302 " ideal model delta sigma weight residual 109.47 178.99 -69.52 3.00e+00 1.11e-01 5.37e+02 angle pdb=" O1 VO4 B 302 " pdb=" V VO4 B 302 " pdb=" O4 VO4 B 302 " ideal model delta sigma weight residual 109.47 178.92 -69.45 3.00e+00 1.11e-01 5.36e+02 angle pdb=" O2 VO4 B 302 " pdb=" V VO4 B 302 " pdb=" O3 VO4 B 302 " ideal model delta sigma weight residual 109.47 177.93 -68.46 3.00e+00 1.11e-01 5.21e+02 angle pdb=" O2 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O3 VO4 E 302 " ideal model delta sigma weight residual 109.47 177.88 -68.41 3.00e+00 1.11e-01 5.20e+02 angle pdb=" O1 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O2 VO4 E 302 " ideal model delta sigma weight residual 109.47 89.52 19.95 3.00e+00 1.11e-01 4.42e+01 ... (remaining 24443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9447 17.93 - 35.86: 967 35.86 - 53.79: 268 53.79 - 71.71: 121 71.71 - 89.64: 25 Dihedral angle restraints: 10828 sinusoidal: 4086 harmonic: 6742 Sorted by residual: dihedral pdb=" CA GLY K 88 " pdb=" C GLY K 88 " pdb=" N LYS K 89 " pdb=" CA LYS K 89 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLY D 133 " pdb=" C GLY D 133 " pdb=" N VAL D 134 " pdb=" CA VAL D 134 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 133 " pdb=" C GLY A 133 " pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 2966 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.278: 0 4.278 - 5.347: 2 Chirality restraints: 2968 Sorted by residual: chirality pdb=" V VO4 E 302 " pdb=" O1 VO4 E 302 " pdb=" O2 VO4 E 302 " pdb=" O4 VO4 E 302 " both_signs ideal model delta sigma weight residual True 5.36 0.02 5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" V VO4 B 302 " pdb=" O1 VO4 B 302 " pdb=" O2 VO4 B 302 " pdb=" O4 VO4 B 302 " both_signs ideal model delta sigma weight residual True 5.36 0.02 5.35 2.00e-01 2.50e+01 7.14e+02 chirality pdb=" CB ILE F 15 " pdb=" CA ILE F 15 " pdb=" CG1 ILE F 15 " pdb=" CG2 ILE F 15 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2965 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 142 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C THR B 142 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 142 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 143 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 142 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C THR E 142 " -0.063 2.00e-02 2.50e+03 pdb=" O THR E 142 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU E 143 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 97 " -0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 98 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.048 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 665 2.66 - 3.22: 17155 3.22 - 3.78: 28154 3.78 - 4.34: 36228 4.34 - 4.90: 57886 Nonbonded interactions: 140088 Sorted by model distance: nonbonded pdb=" O GLY I 155 " pdb=" CG GLU I 156 " model vdw 2.101 3.440 nonbonded pdb=" CA LEU C 61 " pdb=" OG1 THR C 64 " model vdw 2.197 3.470 nonbonded pdb=" CG1 VAL H 76 " pdb=" OE1 GLN I 97 " model vdw 2.202 3.460 nonbonded pdb=" OE2 GLU K 186 " pdb=" CE MET L 147 " model vdw 2.208 3.460 nonbonded pdb=" CA GLY D 8 " pdb=" CG1 VAL L 10 " model vdw 2.211 3.860 ... (remaining 140083 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.010 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.021 0.918 18044 Z= 1.030 Angle : 1.527 69.522 24448 Z= 0.788 Chirality : 0.151 5.347 2968 Planarity : 0.007 0.085 3102 Dihedral : 17.850 89.643 6500 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 1.36 % Allowed : 11.40 % Favored : 87.23 % Rotamer: Outliers : 9.93 % Allowed : 12.49 % Favored : 77.59 % 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 aren not related in a simple way. whole: -5.59 (0.12), residues: 2350 helix: -4.25 (0.09), residues: 937 sheet: -2.71 (0.30), residues: 240 loop : -3.46 (0.15), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 62 TYR 0.023 0.003 TYR J 145 PHE 0.046 0.003 PHE F 17 TRP 0.014 0.002 TRP A 146 HIS 0.010 0.003 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.02064 (18044) covalent geometry : angle 1.52676 (24448) hydrogen bonds : bond 0.30357 ( 682) hydrogen bonds : angle 11.27578 ( 1998) *********************** 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 553 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 367 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8281 (m110) cc_final: 0.8053 (p0) REVERT: A 70 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7111 (tm-30) REVERT: A 168 LYS cc_start: 0.8296 (tttm) cc_final: 0.7969 (ttmm) REVERT: A 179 GLU cc_start: 0.8514 (mp0) cc_final: 0.8249 (mp0) REVERT: B 81 SER cc_start: 0.6952 (OUTLIER) cc_final: 0.6638 (t) REVERT: B 219 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5741 (m-80) REVERT: C 10 VAL cc_start: -0.0816 (OUTLIER) cc_final: -0.1369 (m) REVERT: C 71 HIS cc_start: 0.7933 (m90) cc_final: 0.7714 (m90) REVERT: C 84 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: D 30 PHE cc_start: 0.7730 (m-80) cc_final: 0.7487 (m-80) REVERT: D 74 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7255 (tp) REVERT: E 146 MET cc_start: 0.9092 (tpp) cc_final: 0.8682 (mmm) REVERT: E 210 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8747 (t) REVERT: E 249 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8728 (mt) REVERT: F 10 VAL cc_start: 0.2270 (OUTLIER) cc_final: 0.1768 (t) REVERT: F 12 SER cc_start: 0.0511 (OUTLIER) cc_final: 0.0153 (t) REVERT: F 35 THR cc_start: 0.5355 (OUTLIER) cc_final: 0.5121 (m) REVERT: F 64 THR cc_start: 0.5496 (OUTLIER) cc_final: 0.4853 (p) REVERT: F 68 SER cc_start: 0.5430 (OUTLIER) cc_final: 0.4277 (m) REVERT: G 61 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8489 (p) REVERT: H 35 ASN cc_start: 0.8961 (p0) cc_final: 0.8670 (p0) REVERT: I 135 ASN cc_start: 0.8295 (t0) cc_final: 0.8064 (t0) REVERT: J 35 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7146 (m-40) REVERT: J 96 GLU cc_start: 0.8759 (mp0) cc_final: 0.8437 (mp0) REVERT: L 10 VAL cc_start: 0.6717 (OUTLIER) cc_final: 0.6496 (t) REVERT: L 26 MET cc_start: 0.7918 (tpt) cc_final: 0.7704 (tpt) outliers start: 186 outliers final: 49 residues processed: 504 average time/residue: 0.1305 time to fit residues: 99.1855 Evaluate side-chains 288 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 219 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 70 GLN B 35 ASN B 83 GLN B 238 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 59 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 217 GLN E 67 GLN E 247 GLN F 3 GLN F 48 HIS F 59 GLN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 ASN J 135 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.096317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.078186 restraints weight = 70192.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079584 restraints weight = 47504.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081069 restraints weight = 30148.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.081155 restraints weight = 25175.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081084 restraints weight = 21688.851| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18044 Z= 0.182 Angle : 0.814 14.370 24448 Z= 0.421 Chirality : 0.046 0.202 2968 Planarity : 0.005 0.063 3102 Dihedral : 9.684 92.201 2638 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.55 % Favored : 89.36 % Rotamer: Outliers : 4.96 % Allowed : 20.33 % Favored : 74.71 % 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 aren not related in a simple way. whole: -4.36 (0.14), residues: 2350 helix: -2.67 (0.12), residues: 1013 sheet: -2.06 (0.32), residues: 234 loop : -3.28 (0.16), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 4 TYR 0.020 0.002 TYR J 169 PHE 0.038 0.002 PHE L 13 TRP 0.015 0.002 TRP D 146 HIS 0.006 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00394 (18044) covalent geometry : angle 0.81407 (24448) hydrogen bonds : bond 0.05476 ( 682) hydrogen bonds : angle 6.24080 ( 1998) *********************** 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 364 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 271 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9013 (tmm) cc_final: 0.8778 (tmm) REVERT: A 70 GLN cc_start: 0.6417 (mm110) cc_final: 0.6217 (tp-100) REVERT: A 186 MET cc_start: 0.7644 (mtm) cc_final: 0.7438 (mtm) REVERT: B 23 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.3797 (tpp80) REVERT: B 146 MET cc_start: 0.8276 (tpp) cc_final: 0.7933 (mmm) REVERT: C 71 HIS cc_start: 0.8325 (m90) cc_final: 0.8016 (m90) REVERT: D 14 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7275 (mmt180) REVERT: D 90 LEU cc_start: 0.8785 (tp) cc_final: 0.8311 (tt) REVERT: D 198 ASN cc_start: 0.7755 (m-40) cc_final: 0.6408 (t0) REVERT: G 46 PHE cc_start: 0.8739 (m-80) cc_final: 0.8420 (m-10) REVERT: I 135 ASN cc_start: 0.8456 (t0) cc_final: 0.8253 (t0) REVERT: J 96 GLU cc_start: 0.8862 (mp0) cc_final: 0.8525 (mp0) REVERT: J 183 MET cc_start: 0.8282 (tpp) cc_final: 0.8065 (mmt) REVERT: K 147 MET cc_start: 0.7495 (ptm) cc_final: 0.6959 (ptm) REVERT: L 24 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5886 (tm) REVERT: L 100 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7694 (tm-30) outliers start: 93 outliers final: 42 residues processed: 345 average time/residue: 0.1131 time to fit residues: 60.4699 Evaluate side-chains 277 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 126 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 231 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 0.0030 chunk 129 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 238 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 71 HIS F 66 GLN K 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.098301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080336 restraints weight = 71354.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.081845 restraints weight = 47699.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082303 restraints weight = 30477.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082545 restraints weight = 29777.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082595 restraints weight = 25796.224| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18044 Z= 0.129 Angle : 0.709 13.258 24448 Z= 0.362 Chirality : 0.043 0.190 2968 Planarity : 0.004 0.053 3102 Dihedral : 7.775 91.016 2563 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.49 % Favored : 90.43 % Rotamer: Outliers : 4.32 % Allowed : 22.47 % Favored : 73.21 % 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 aren not related in a simple way. whole: -3.50 (0.15), residues: 2350 helix: -1.64 (0.14), residues: 1025 sheet: -1.70 (0.32), residues: 258 loop : -3.18 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.018 0.001 TYR J 145 PHE 0.028 0.001 PHE C 17 TRP 0.011 0.001 TRP C 60 HIS 0.009 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00271 (18044) covalent geometry : angle 0.70927 (24448) hydrogen bonds : bond 0.04239 ( 682) hydrogen bonds : angle 5.51328 ( 1998) *********************** 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 365 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9038 (tmm) cc_final: 0.8737 (tmm) REVERT: A 70 GLN cc_start: 0.6392 (mm110) cc_final: 0.6149 (tp-100) REVERT: A 125 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7504 (mm-40) REVERT: A 186 MET cc_start: 0.7543 (mtm) cc_final: 0.7314 (mtm) REVERT: C 71 HIS cc_start: 0.8248 (m-70) cc_final: 0.7758 (m90) REVERT: D 14 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6761 (mmt180) REVERT: D 45 MET cc_start: 0.8393 (mmm) cc_final: 0.8165 (mtp) REVERT: D 228 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7037 (tt) REVERT: G 46 PHE cc_start: 0.8656 (m-80) cc_final: 0.8319 (m-10) REVERT: G 96 GLU cc_start: 0.8602 (tp30) cc_final: 0.8298 (tp30) REVERT: H 4 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5682 (tpp-160) REVERT: H 35 ASN cc_start: 0.8765 (p0) cc_final: 0.8545 (p0) REVERT: I 4 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6129 (ttp80) REVERT: J 96 GLU cc_start: 0.8777 (mp0) cc_final: 0.8483 (mp0) REVERT: L 24 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.5513 (tm) REVERT: L 100 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7881 (tm-30) REVERT: L 147 MET cc_start: 0.9011 (ppp) cc_final: 0.8604 (ppp) outliers start: 81 outliers final: 50 residues processed: 345 average time/residue: 0.1117 time to fit residues: 60.1333 Evaluate side-chains 295 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.096135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077982 restraints weight = 69466.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079415 restraints weight = 45753.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079721 restraints weight = 30556.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080165 restraints weight = 28696.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080284 restraints weight = 24814.715| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18044 Z= 0.149 Angle : 0.705 12.062 24448 Z= 0.359 Chirality : 0.044 0.202 2968 Planarity : 0.004 0.052 3102 Dihedral : 7.458 93.974 2557 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.83 % Favored : 90.09 % Rotamer: Outliers : 4.80 % Allowed : 23.91 % Favored : 71.29 % 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 aren not related in a simple way. whole: -3.00 (0.16), residues: 2350 helix: -1.12 (0.15), residues: 1001 sheet: -1.50 (0.32), residues: 266 loop : -3.00 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.015 0.001 TYR J 145 PHE 0.042 0.002 PHE L 13 TRP 0.019 0.002 TRP A 6 HIS 0.007 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00328 (18044) covalent geometry : angle 0.70545 (24448) hydrogen bonds : bond 0.03991 ( 682) hydrogen bonds : angle 5.29530 ( 1998) *********************** 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 351 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 261 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7943 (t80) cc_final: 0.7543 (t80) REVERT: A 70 GLN cc_start: 0.6671 (mm110) cc_final: 0.6283 (tp-100) REVERT: A 94 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6945 (ttm170) REVERT: A 124 GLU cc_start: 0.7326 (mp0) cc_final: 0.6808 (mp0) REVERT: A 125 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7694 (mm-40) REVERT: A 139 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 186 MET cc_start: 0.7744 (mtm) cc_final: 0.7434 (mtm) REVERT: B 146 MET cc_start: 0.7794 (mmp) cc_final: 0.7451 (tpp) REVERT: C 71 HIS cc_start: 0.8419 (m-70) cc_final: 0.7952 (m90) REVERT: C 79 MET cc_start: 0.8612 (mmm) cc_final: 0.8347 (mmm) REVERT: D 14 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6828 (mmt180) REVERT: D 45 MET cc_start: 0.8522 (mmm) cc_final: 0.8310 (mtp) REVERT: D 93 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8297 (mm) REVERT: D 228 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7110 (tt) REVERT: E 146 MET cc_start: 0.8452 (tpp) cc_final: 0.8194 (mmm) REVERT: E 157 ARG cc_start: 0.5949 (ttt-90) cc_final: 0.5509 (ttt90) REVERT: G 46 PHE cc_start: 0.8728 (m-80) cc_final: 0.8381 (m-10) REVERT: G 134 MET cc_start: 0.8173 (ptt) cc_final: 0.7932 (ptt) REVERT: H 4 ARG cc_start: 0.5968 (ttt180) cc_final: 0.5552 (tpp-160) REVERT: I 4 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6655 (ttp80) REVERT: K 147 MET cc_start: 0.7502 (ptm) cc_final: 0.7139 (ptm) REVERT: L 24 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5751 (tm) REVERT: L 47 ASP cc_start: 0.8369 (p0) cc_final: 0.8121 (p0) REVERT: L 100 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7965 (tm-30) outliers start: 90 outliers final: 56 residues processed: 330 average time/residue: 0.1185 time to fit residues: 60.2295 Evaluate side-chains 294 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 227 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 6 ASN F 63 GLN F 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075815 restraints weight = 70463.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077120 restraints weight = 46398.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077534 restraints weight = 30646.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077806 restraints weight = 30021.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077953 restraints weight = 26049.125| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18044 Z= 0.206 Angle : 0.758 11.685 24448 Z= 0.384 Chirality : 0.045 0.197 2968 Planarity : 0.004 0.051 3102 Dihedral : 7.232 100.533 2550 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.15 % Rotamer: Outliers : 5.60 % Allowed : 24.12 % Favored : 70.28 % 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 aren not related in a simple way. whole: -2.87 (0.16), residues: 2350 helix: -0.98 (0.15), residues: 1002 sheet: -1.45 (0.33), residues: 248 loop : -2.95 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 67 TYR 0.015 0.002 TYR G 158 PHE 0.040 0.002 PHE L 13 TRP 0.016 0.002 TRP A 6 HIS 0.007 0.002 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00453 (18044) covalent geometry : angle 0.75789 (24448) hydrogen bonds : bond 0.04170 ( 682) hydrogen bonds : angle 5.39746 ( 1998) *********************** 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 337 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 232 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7986 (t80) cc_final: 0.7712 (t80) REVERT: A 70 GLN cc_start: 0.6879 (mm110) cc_final: 0.6432 (tp-100) REVERT: A 125 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7683 (mm-40) REVERT: A 254 MET cc_start: 0.7580 (mmm) cc_final: 0.6862 (mmm) REVERT: C 71 HIS cc_start: 0.8498 (m-70) cc_final: 0.8231 (m90) REVERT: C 79 MET cc_start: 0.8673 (mmm) cc_final: 0.8467 (mmm) REVERT: D 14 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6572 (mmt180) REVERT: E 146 MET cc_start: 0.8579 (tpp) cc_final: 0.8162 (mmm) REVERT: E 264 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: F 7 GLN cc_start: 0.1814 (OUTLIER) cc_final: 0.1605 (pt0) REVERT: G 46 PHE cc_start: 0.8811 (m-80) cc_final: 0.8460 (m-10) REVERT: G 134 MET cc_start: 0.8225 (ptt) cc_final: 0.7944 (ptt) REVERT: H 4 ARG cc_start: 0.5983 (ttt180) cc_final: 0.5595 (tpp80) REVERT: J 60 MET cc_start: 0.7830 (tpp) cc_final: 0.7499 (ttt) REVERT: K 147 MET cc_start: 0.7648 (ptm) cc_final: 0.7293 (ptm) REVERT: L 24 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5696 (tm) REVERT: L 47 ASP cc_start: 0.8374 (p0) cc_final: 0.8098 (p0) REVERT: L 100 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8128 (tm-30) outliers start: 105 outliers final: 67 residues processed: 317 average time/residue: 0.1196 time to fit residues: 59.8064 Evaluate side-chains 293 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 133 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN I 135 ASN ** L 128 GLN ** 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 = 0.3701 r_free = 0.3701 target = 0.093210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075897 restraints weight = 70522.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076079 restraints weight = 47310.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077020 restraints weight = 36551.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.077350 restraints weight = 29048.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077408 restraints weight = 27050.162| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18044 Z= 0.219 Angle : 0.771 11.660 24448 Z= 0.390 Chirality : 0.045 0.212 2968 Planarity : 0.005 0.061 3102 Dihedral : 7.166 104.103 2545 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.28 % Rotamer: Outliers : 5.55 % Allowed : 25.24 % Favored : 69.21 % 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 aren not related in a simple way. whole: -2.82 (0.16), residues: 2350 helix: -0.88 (0.15), residues: 991 sheet: -1.29 (0.34), residues: 248 loop : -3.01 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 94 TYR 0.014 0.002 TYR G 158 PHE 0.046 0.002 PHE L 13 TRP 0.015 0.002 TRP A 6 HIS 0.023 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00484 (18044) covalent geometry : angle 0.77105 (24448) hydrogen bonds : bond 0.04133 ( 682) hydrogen bonds : angle 5.40519 ( 1998) *********************** 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 340 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 236 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8383 (mtt) cc_final: 0.8152 (mtt) REVERT: A 70 GLN cc_start: 0.6702 (mm110) cc_final: 0.6381 (tp-100) REVERT: A 125 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7647 (mm-40) REVERT: A 254 MET cc_start: 0.7585 (mmm) cc_final: 0.7129 (mmm) REVERT: D 14 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6506 (mmt180) REVERT: D 31 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6873 (p) REVERT: E 146 MET cc_start: 0.8588 (tpp) cc_final: 0.8153 (mmm) REVERT: E 264 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: G 46 PHE cc_start: 0.8859 (m-80) cc_final: 0.8447 (m-10) REVERT: G 69 ASP cc_start: 0.8116 (t0) cc_final: 0.7894 (t0) REVERT: G 134 MET cc_start: 0.8192 (ptt) cc_final: 0.7901 (ptt) REVERT: H 4 ARG cc_start: 0.5998 (ttt180) cc_final: 0.5661 (tpp80) REVERT: J 15 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8260 (mt) REVERT: J 60 MET cc_start: 0.7902 (tpp) cc_final: 0.7664 (ttt) REVERT: J 93 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: K 147 MET cc_start: 0.7632 (ptm) cc_final: 0.7333 (ptm) REVERT: L 24 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5756 (tm) REVERT: L 26 MET cc_start: 0.8316 (tpt) cc_final: 0.8063 (tpt) REVERT: L 47 ASP cc_start: 0.8388 (p0) cc_final: 0.8076 (p0) REVERT: L 100 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8151 (tm-30) REVERT: L 147 MET cc_start: 0.8890 (ppp) cc_final: 0.8570 (ppp) outliers start: 104 outliers final: 78 residues processed: 316 average time/residue: 0.1326 time to fit residues: 64.9922 Evaluate side-chains 305 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 224 optimal weight: 0.0980 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 100 optimal weight: 7.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.093698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.076361 restraints weight = 70692.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076647 restraints weight = 46783.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.077398 restraints weight = 36642.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077967 restraints weight = 30182.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078019 restraints weight = 26645.448| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18044 Z= 0.185 Angle : 0.746 11.772 24448 Z= 0.376 Chirality : 0.045 0.182 2968 Planarity : 0.004 0.060 3102 Dihedral : 6.871 105.813 2541 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.15 % Rotamer: Outliers : 5.23 % Allowed : 26.36 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.16), residues: 2350 helix: -0.71 (0.16), residues: 985 sheet: -1.44 (0.33), residues: 261 loop : -2.92 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 193 TYR 0.013 0.002 TYR J 145 PHE 0.046 0.002 PHE L 13 TRP 0.013 0.002 TRP A 6 HIS 0.028 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00410 (18044) covalent geometry : angle 0.74596 (24448) hydrogen bonds : bond 0.03922 ( 682) hydrogen bonds : angle 5.32173 ( 1998) *********************** 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 338 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 240 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8413 (mtt) cc_final: 0.8203 (mtt) REVERT: A 125 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7604 (mm-40) REVERT: A 254 MET cc_start: 0.7591 (mmm) cc_final: 0.7145 (mmm) REVERT: B 80 MET cc_start: 0.6194 (ppp) cc_final: 0.5884 (ppp) REVERT: D 14 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6025 (mmt180) REVERT: E 146 MET cc_start: 0.8583 (tpp) cc_final: 0.8109 (mmm) REVERT: E 264 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: F 47 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: G 46 PHE cc_start: 0.8806 (m-80) cc_final: 0.8378 (m-10) REVERT: G 134 MET cc_start: 0.8137 (ptt) cc_final: 0.7857 (ptt) REVERT: H 4 ARG cc_start: 0.5946 (ttt180) cc_final: 0.5704 (tpp80) REVERT: H 180 GLN cc_start: 0.8826 (tp40) cc_final: 0.8428 (tm-30) REVERT: J 15 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (mt) REVERT: J 60 MET cc_start: 0.7860 (tpp) cc_final: 0.7605 (ttt) REVERT: J 93 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: J 150 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.9014 (m) REVERT: K 147 MET cc_start: 0.7561 (ptm) cc_final: 0.7216 (ptm) REVERT: L 24 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6007 (tm) REVERT: L 47 ASP cc_start: 0.8344 (p0) cc_final: 0.8055 (p0) REVERT: L 85 ASP cc_start: 0.7847 (m-30) cc_final: 0.7607 (m-30) REVERT: L 100 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8132 (tm-30) REVERT: L 147 MET cc_start: 0.8940 (ppp) cc_final: 0.8729 (ppp) outliers start: 98 outliers final: 74 residues processed: 317 average time/residue: 0.1258 time to fit residues: 63.0099 Evaluate side-chains 302 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 221 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 151 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 0.0980 chunk 175 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076817 restraints weight = 70304.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078103 restraints weight = 46697.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078468 restraints weight = 30663.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078837 restraints weight = 30446.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078992 restraints weight = 26406.553| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18044 Z= 0.149 Angle : 0.714 11.838 24448 Z= 0.360 Chirality : 0.044 0.187 2968 Planarity : 0.004 0.052 3102 Dihedral : 6.729 105.487 2541 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.74 % Favored : 90.17 % Rotamer: Outliers : 4.54 % Allowed : 27.32 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.17), residues: 2350 helix: -0.48 (0.16), residues: 996 sheet: -1.37 (0.33), residues: 257 loop : -2.88 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 55 TYR 0.014 0.001 TYR J 145 PHE 0.048 0.002 PHE L 13 TRP 0.020 0.002 TRP F 60 HIS 0.023 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00330 (18044) covalent geometry : angle 0.71400 (24448) hydrogen bonds : bond 0.03649 ( 682) hydrogen bonds : angle 5.17070 ( 1998) *********************** 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 320 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7667 (mm-40) REVERT: B 80 MET cc_start: 0.6408 (ppp) cc_final: 0.6042 (ppp) REVERT: D 14 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6208 (mmt180) REVERT: D 31 SER cc_start: 0.6912 (OUTLIER) cc_final: 0.6674 (p) REVERT: D 131 MET cc_start: 0.7792 (tpp) cc_final: 0.7524 (mmt) REVERT: E 264 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: F 47 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6291 (pp20) REVERT: G 46 PHE cc_start: 0.8757 (m-80) cc_final: 0.8363 (m-10) REVERT: G 134 MET cc_start: 0.8146 (ptt) cc_final: 0.7851 (ptt) REVERT: H 4 ARG cc_start: 0.6008 (ttt180) cc_final: 0.5788 (tpp80) REVERT: H 180 GLN cc_start: 0.8789 (tp40) cc_final: 0.8388 (tm-30) REVERT: J 15 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8135 (mt) REVERT: J 60 MET cc_start: 0.7823 (tpp) cc_final: 0.7550 (ttt) REVERT: J 93 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: K 147 MET cc_start: 0.7508 (ptm) cc_final: 0.7273 (ptm) REVERT: L 24 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6018 (tm) REVERT: L 85 ASP cc_start: 0.7821 (m-30) cc_final: 0.7550 (m-30) REVERT: L 100 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7999 (tm-30) REVERT: L 134 MET cc_start: 0.7098 (ptp) cc_final: 0.6682 (mpp) outliers start: 85 outliers final: 70 residues processed: 304 average time/residue: 0.1117 time to fit residues: 53.8240 Evaluate side-chains 293 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 216 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 147 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 226 optimal weight: 0.0980 chunk 204 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.095375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077403 restraints weight = 69873.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078638 restraints weight = 46273.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079194 restraints weight = 31270.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079503 restraints weight = 28851.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079518 restraints weight = 25404.788| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18044 Z= 0.139 Angle : 0.732 11.955 24448 Z= 0.364 Chirality : 0.044 0.177 2968 Planarity : 0.004 0.049 3102 Dihedral : 6.636 105.577 2540 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 4.64 % Allowed : 27.48 % Favored : 67.88 % 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 aren not related in a simple way. whole: -2.38 (0.17), residues: 2350 helix: -0.41 (0.16), residues: 1003 sheet: -1.32 (0.33), residues: 257 loop : -2.85 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.018 0.001 TYR I 169 PHE 0.051 0.002 PHE L 13 TRP 0.027 0.002 TRP F 60 HIS 0.033 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00311 (18044) covalent geometry : angle 0.73165 (24448) hydrogen bonds : bond 0.03549 ( 682) hydrogen bonds : angle 5.12838 ( 1998) *********************** 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 314 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7726 (mm-40) REVERT: B 80 MET cc_start: 0.6571 (ppp) cc_final: 0.6150 (ppp) REVERT: C 21 GLU cc_start: 0.2963 (OUTLIER) cc_final: 0.2277 (pm20) REVERT: D 14 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5723 (mmt180) REVERT: D 31 SER cc_start: 0.7048 (OUTLIER) cc_final: 0.6795 (p) REVERT: E 146 MET cc_start: 0.8234 (tpp) cc_final: 0.7977 (mmm) REVERT: E 264 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: F 47 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6474 (pp20) REVERT: G 12 ILE cc_start: 0.8381 (tt) cc_final: 0.8019 (tp) REVERT: G 46 PHE cc_start: 0.8735 (m-80) cc_final: 0.8343 (m-10) REVERT: G 134 MET cc_start: 0.8141 (ptt) cc_final: 0.7846 (ptt) REVERT: H 180 GLN cc_start: 0.8776 (tp40) cc_final: 0.8386 (tm-30) REVERT: J 60 MET cc_start: 0.7812 (tpp) cc_final: 0.7539 (ttt) REVERT: J 93 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: K 147 MET cc_start: 0.7484 (ptm) cc_final: 0.7220 (ptt) REVERT: L 24 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6070 (tm) REVERT: L 100 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7991 (tm-30) outliers start: 87 outliers final: 69 residues processed: 300 average time/residue: 0.1221 time to fit residues: 57.6793 Evaluate side-chains 293 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 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 = 0.3705 r_free = 0.3705 target = 0.093506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074740 restraints weight = 71011.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076292 restraints weight = 44606.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.077341 restraints weight = 32690.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078048 restraints weight = 26656.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078360 restraints weight = 23374.547| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18044 Z= 0.207 Angle : 0.789 11.921 24448 Z= 0.395 Chirality : 0.046 0.208 2968 Planarity : 0.004 0.048 3102 Dihedral : 6.800 109.739 2540 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.23 % Favored : 88.68 % Rotamer: Outliers : 4.32 % Allowed : 27.96 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.16), residues: 2350 helix: -0.57 (0.16), residues: 988 sheet: -1.25 (0.33), residues: 248 loop : -2.87 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 94 TYR 0.016 0.002 TYR J 145 PHE 0.052 0.002 PHE L 13 TRP 0.037 0.003 TRP F 60 HIS 0.021 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00462 (18044) covalent geometry : angle 0.78857 (24448) hydrogen bonds : bond 0.04001 ( 682) hydrogen bonds : angle 5.33393 ( 1998) ********************** 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 301 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7739 (mm-40) REVERT: B 80 MET cc_start: 0.6577 (ppp) cc_final: 0.6057 (ppp) REVERT: C 21 GLU cc_start: 0.2583 (OUTLIER) cc_final: 0.1909 (pm20) REVERT: D 14 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.5766 (mmt180) REVERT: D 31 SER cc_start: 0.6899 (OUTLIER) cc_final: 0.6674 (p) REVERT: E 146 MET cc_start: 0.8467 (tpp) cc_final: 0.8154 (mmm) REVERT: E 264 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: F 7 GLN cc_start: 0.2225 (OUTLIER) cc_final: 0.1958 (pt0) REVERT: F 47 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6582 (pp20) REVERT: G 46 PHE cc_start: 0.8753 (m-80) cc_final: 0.8322 (m-10) REVERT: G 134 MET cc_start: 0.8093 (ptt) cc_final: 0.7859 (ptt) REVERT: H 180 GLN cc_start: 0.8837 (tp40) cc_final: 0.8322 (tm-30) REVERT: I 169 TYR cc_start: 0.8355 (m-10) cc_final: 0.8130 (m-10) REVERT: J 60 MET cc_start: 0.7924 (tpp) cc_final: 0.7679 (ttt) REVERT: J 93 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: K 147 MET cc_start: 0.7549 (ptm) cc_final: 0.7235 (ptt) REVERT: L 24 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6128 (tm) REVERT: L 100 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8103 (tm-30) REVERT: L 134 MET cc_start: 0.6749 (ptp) cc_final: 0.6454 (tmm) REVERT: L 147 MET cc_start: 0.8728 (ppp) cc_final: 0.8523 (ppp) outliers start: 81 outliers final: 66 residues processed: 287 average time/residue: 0.1066 time to fit residues: 49.4482 Evaluate side-chains 287 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 213 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 19 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 180 optimal weight: 0.1980 chunk 224 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 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 = 0.3717 r_free = 0.3717 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076073 restraints weight = 70560.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077339 restraints weight = 47981.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077666 restraints weight = 31569.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078241 restraints weight = 31044.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078314 restraints weight = 26867.979| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18044 Z= 0.174 Angle : 0.770 12.269 24448 Z= 0.384 Chirality : 0.045 0.174 2968 Planarity : 0.004 0.049 3102 Dihedral : 6.707 110.920 2540 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.09 % Favored : 89.83 % Rotamer: Outliers : 4.06 % Allowed : 28.28 % Favored : 67.66 % 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 aren not related in a simple way. whole: -2.47 (0.17), residues: 2350 helix: -0.52 (0.16), residues: 997 sheet: -1.36 (0.33), residues: 257 loop : -2.83 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.017 0.001 TYR J 145 PHE 0.053 0.002 PHE L 13 TRP 0.029 0.002 TRP F 60 HIS 0.020 0.002 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00390 (18044) covalent geometry : angle 0.77028 (24448) hydrogen bonds : bond 0.03828 ( 682) hydrogen bonds : angle 5.25585 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.62 seconds wall clock time: 46 minutes 15.71 seconds (2775.71 seconds total)