Starting phenix.real_space_refine on Sun Jul 5 07:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.map" model { file = "/net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d61_30587/07_2026/7d61_30587.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "E" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 5.40, per 1000 atoms: 0.20 Number of scatterers: 26664 At special positions: 0 Unit cell: (160.6, 161.7, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 0 sheets defined 73.2% alpha, 0.0% 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 7 through 14 removed outlier: 3.797A pdb=" N GLN A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.610A pdb=" N THR A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 69 removed outlier: 3.628A pdb=" N LEU A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.577A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.172A pdb=" N TRP A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.748A pdb=" N ILE A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 removed outlier: 3.587A pdb=" N TYR A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.890A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.554A pdb=" N CYS A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 4.104A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 4.073A pdb=" N TRP A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.711A pdb=" N LYS A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.549A pdb=" N GLU A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.626A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 204 removed outlier: 3.536A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 247 removed outlier: 3.505A pdb=" N PHE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.516A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.788A pdb=" N GLN B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.557A pdb=" N THR B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 52 through 69 removed outlier: 3.729A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.678A pdb=" N LEU B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 4.059A pdb=" N TRP B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.738A pdb=" N ILE B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.658A pdb=" N TYR B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.828A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.527A pdb=" N CYS B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 4.053A pdb=" N ILE B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 4.059A pdb=" N TRP B 150 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.719A pdb=" N LYS B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.553A pdb=" N GLU B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 204 removed outlier: 3.554A pdb=" N ILE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 247 removed outlier: 3.601A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 279 through 288 removed outlier: 3.564A pdb=" N VAL B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.793A pdb=" N GLN C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 38 removed outlier: 3.616A pdb=" N THR C 27 " --> pdb=" O MET C 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.732A pdb=" N PHE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.598A pdb=" N LEU C 62 " --> pdb=" O PRO C 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.129A pdb=" N TRP C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.747A pdb=" N ILE C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.585A pdb=" N TYR C 98 " --> pdb=" O CYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.754A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 removed outlier: 4.196A pdb=" N GLY C 131 " --> pdb=" O CYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 4.014A pdb=" N ILE C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 4.063A pdb=" N TRP C 150 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.728A pdb=" N LYS C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.583A pdb=" N GLU C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 204 removed outlier: 3.525A pdb=" N ILE C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 192 " --> pdb=" O CYS C 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 247 removed outlier: 3.547A pdb=" N THR C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 239 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'D' and resid 7 through 13 Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.568A pdb=" N THR D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.723A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 3.608A pdb=" N LEU D 62 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 4.091A pdb=" N TRP D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.621A pdb=" N ILE D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 108 removed outlier: 3.543A pdb=" N TYR D 98 " --> pdb=" O CYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.843A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 131 removed outlier: 3.658A pdb=" N CYS D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 131 " --> pdb=" O CYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 4.032A pdb=" N ILE D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.982A pdb=" N TRP D 150 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.721A pdb=" N LYS D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 204 removed outlier: 3.503A pdb=" N ILE D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 192 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 247 removed outlier: 3.566A pdb=" N PHE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'E' and resid 7 through 14 removed outlier: 3.795A pdb=" N GLN E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 38 removed outlier: 3.595A pdb=" N THR E 27 " --> pdb=" O MET E 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 69 removed outlier: 3.529A pdb=" N LEU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.722A pdb=" N LEU E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 4.061A pdb=" N TRP E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.850A pdb=" N ILE E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.708A pdb=" N TYR E 98 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.836A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.653A pdb=" N CYS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY E 131 " --> pdb=" O CYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 removed outlier: 4.007A pdb=" N ILE E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 4.078A pdb=" N TRP E 150 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.731A pdb=" N LYS E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 removed outlier: 3.513A pdb=" N LYS E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 204 removed outlier: 3.522A pdb=" N ILE E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E 192 " --> pdb=" O CYS E 188 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 247 removed outlier: 3.537A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 247 " --> pdb=" O LYS E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 265 Processing helix chain 'E' and resid 279 through 288 Processing helix chain 'F' and resid 7 through 14 removed outlier: 3.718A pdb=" N GLN F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 38 removed outlier: 3.630A pdb=" N THR F 27 " --> pdb=" O MET F 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 69 removed outlier: 3.611A pdb=" N LEU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.556A pdb=" N LEU F 62 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 removed outlier: 4.103A pdb=" N TRP F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.771A pdb=" N ILE F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.523A pdb=" N TYR F 98 " --> pdb=" O CYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 118 removed outlier: 3.749A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 131 removed outlier: 3.568A pdb=" N CYS F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 4.003A pdb=" N ILE F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 removed outlier: 4.088A pdb=" N TRP F 150 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.703A pdb=" N LYS F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.588A pdb=" N GLU F 170 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 204 removed outlier: 3.531A pdb=" N ILE F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 247 removed outlier: 3.509A pdb=" N PHE F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 247 " --> pdb=" O LYS F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 265 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.544A pdb=" N VAL F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 14 removed outlier: 3.794A pdb=" N GLN G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 38 removed outlier: 3.654A pdb=" N THR G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.578A pdb=" N LEU G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 69 removed outlier: 3.737A pdb=" N PHE G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 3.726A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 removed outlier: 4.063A pdb=" N TRP G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.648A pdb=" N ILE G 87 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 108 removed outlier: 3.600A pdb=" N TYR G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.928A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 131 removed outlier: 3.835A pdb=" N GLU G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY G 131 " --> pdb=" O CYS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 removed outlier: 4.007A pdb=" N ILE G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.972A pdb=" N TRP G 150 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.780A pdb=" N LYS G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.568A pdb=" N LYS G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 204 removed outlier: 3.526A pdb=" N ILE G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 247 removed outlier: 3.579A pdb=" N PHE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 217 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU G 239 " --> pdb=" O ASN G 235 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 243 " --> pdb=" O GLU G 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 247 " --> pdb=" O LYS G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 265 Processing helix chain 'G' and resid 279 through 288 Processing helix chain 'H' and resid 7 through 14 removed outlier: 3.813A pdb=" N GLN H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 38 removed outlier: 3.568A pdb=" N THR H 27 " --> pdb=" O MET H 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 removed outlier: 3.702A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.642A pdb=" N LEU H 62 " --> pdb=" O PRO H 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 removed outlier: 4.060A pdb=" N TRP H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.687A pdb=" N ILE H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 108 removed outlier: 3.530A pdb=" N TYR H 98 " --> pdb=" O CYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 120 removed outlier: 3.779A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 131 removed outlier: 3.676A pdb=" N CYS H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 131 " --> pdb=" O CYS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 142 removed outlier: 4.102A pdb=" N ILE H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 removed outlier: 4.038A pdb=" N TRP H 150 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.753A pdb=" N LYS H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 204 removed outlier: 3.512A pdb=" N ILE H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE H 192 " --> pdb=" O CYS H 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 247 removed outlier: 3.524A pdb=" N PHE H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 239 " --> pdb=" O ASN H 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU H 247 " --> pdb=" O LYS H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 279 through 288 Processing helix chain 'I' and resid 7 through 14 removed outlier: 3.755A pdb=" N GLN I 14 " --> pdb=" O PHE I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 38 removed outlier: 3.678A pdb=" N THR I 27 " --> pdb=" O MET I 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 52 through 69 removed outlier: 3.744A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.644A pdb=" N LEU I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 removed outlier: 4.145A pdb=" N TRP I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 107 removed outlier: 3.569A pdb=" N TYR I 98 " --> pdb=" O CYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 118 removed outlier: 3.838A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 131 removed outlier: 3.797A pdb=" N GLU I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER I 130 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY I 131 " --> pdb=" O CYS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 142 removed outlier: 4.131A pdb=" N ILE I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 4.120A pdb=" N TRP I 150 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.719A pdb=" N LYS I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 204 removed outlier: 3.508A pdb=" N ILE I 181 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I 192 " --> pdb=" O CYS I 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 247 removed outlier: 3.601A pdb=" N THR I 217 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I 239 " --> pdb=" O ASN I 235 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS I 243 " --> pdb=" O GLU I 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU I 247 " --> pdb=" O LYS I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 265 Processing helix chain 'I' and resid 279 through 288 removed outlier: 3.526A pdb=" N VAL I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 14 removed outlier: 3.729A pdb=" N GLN J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 38 removed outlier: 3.634A pdb=" N THR J 27 " --> pdb=" O MET J 23 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 69 removed outlier: 3.656A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.699A pdb=" N LEU J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 78 removed outlier: 4.182A pdb=" N TRP J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.677A pdb=" N ILE J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 108 removed outlier: 3.600A pdb=" N TYR J 98 " --> pdb=" O CYS J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 120 removed outlier: 3.889A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 130 removed outlier: 3.586A pdb=" N CYS J 127 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 130 " --> pdb=" O GLU J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 removed outlier: 4.005A pdb=" N TRP J 150 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.731A pdb=" N LYS J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 171 removed outlier: 3.599A pdb=" N GLU J 170 " --> pdb=" O THR J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 204 removed outlier: 3.554A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE J 192 " --> pdb=" O CYS J 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 247 removed outlier: 3.534A pdb=" N PHE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 239 " --> pdb=" O ASN J 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU J 247 " --> pdb=" O LYS J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 265 removed outlier: 3.518A pdb=" N ALA J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 288 Processing helix chain 'K' and resid 7 through 14 removed outlier: 3.752A pdb=" N GLN K 14 " --> pdb=" O PHE K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 38 removed outlier: 3.635A pdb=" N THR K 27 " --> pdb=" O MET K 23 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 35 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 52 Processing helix chain 'K' and resid 52 through 69 removed outlier: 3.715A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.619A pdb=" N LEU K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 78 removed outlier: 4.183A pdb=" N TRP K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.513A pdb=" N LYS K 86 " --> pdb=" O ASN K 83 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'K' and resid 94 through 107 removed outlier: 3.570A pdb=" N TYR K 98 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 118 removed outlier: 3.841A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.761A pdb=" N GLU K 126 " --> pdb=" O GLY K 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS K 127 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY K 131 " --> pdb=" O CYS K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 removed outlier: 4.106A pdb=" N TRP K 150 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 156 removed outlier: 3.763A pdb=" N LYS K 155 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 171 removed outlier: 3.646A pdb=" N GLU K 170 " --> pdb=" O THR K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 176 removed outlier: 3.562A pdb=" N LEU K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 204 removed outlier: 3.565A pdb=" N ILE K 181 " --> pdb=" O ALA K 177 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 192 " --> pdb=" O CYS K 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 247 removed outlier: 3.535A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU K 239 " --> pdb=" O ASN K 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU K 247 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 265 Processing helix chain 'K' and resid 279 through 288 1120 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.44: 7952 1.44 - 1.56: 15049 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" C12 PA8 H 305 " pdb=" O7 PA8 H 305 " ideal model delta sigma weight residual 1.327 1.407 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C12 PA8 K 305 " pdb=" O7 PA8 K 305 " ideal model delta sigma weight residual 1.327 1.406 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C12 PA8 D 305 " pdb=" O7 PA8 D 305 " ideal model delta sigma weight residual 1.327 1.406 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C12 PA8 C 305 " pdb=" O7 PA8 C 305 " ideal model delta sigma weight residual 1.327 1.406 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C12 PA8 F 305 " pdb=" O7 PA8 F 305 " ideal model delta sigma weight residual 1.327 1.405 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 35184 2.14 - 4.28: 885 4.28 - 6.42: 488 6.42 - 8.56: 82 8.56 - 10.70: 134 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE C 7 " pdb=" CA ILE C 7 " pdb=" C ILE C 7 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C GLY E 136 " pdb=" N LEU E 137 " pdb=" CA LEU E 137 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLY G 136 " pdb=" N LEU G 137 " pdb=" CA LEU G 137 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLY F 136 " pdb=" N LEU F 137 " pdb=" CA LEU F 137 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C5 PA8 J 303 " pdb=" C4 PA8 J 303 " pdb=" O5 PA8 J 303 " ideal model delta sigma weight residual 111.20 120.67 -9.47 3.00e+00 1.11e-01 9.97e+00 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 13161 15.11 - 30.22: 2109 30.22 - 45.33: 601 45.33 - 60.44: 101 60.44 - 75.55: 33 Dihedral angle restraints: 16005 sinusoidal: 6743 harmonic: 9262 Sorted by residual: dihedral pdb=" CA PRO J 165 " pdb=" C PRO J 165 " pdb=" N THR J 166 " pdb=" CA THR J 166 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO K 165 " pdb=" C PRO K 165 " pdb=" N THR K 166 " pdb=" CA THR K 166 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO D 165 " pdb=" C PRO D 165 " pdb=" N THR D 166 " pdb=" CA THR D 166 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 16002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2131 0.031 - 0.062: 1277 0.062 - 0.093: 314 0.093 - 0.124: 141 0.124 - 0.155: 53 Chirality restraints: 3916 Sorted by residual: chirality pdb=" C2 PA8 A 302 " pdb=" C1 PA8 A 302 " pdb=" C3 PA8 A 302 " pdb=" O7 PA8 A 302 " both_signs ideal model delta sigma weight residual False -2.37 -2.53 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" C2 PA8 B 302 " pdb=" C1 PA8 B 302 " pdb=" C3 PA8 B 302 " pdb=" O7 PA8 B 302 " both_signs ideal model delta sigma weight residual False -2.37 -2.53 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" C2 PA8 K 302 " pdb=" C1 PA8 K 302 " pdb=" C3 PA8 K 302 " pdb=" O7 PA8 K 302 " both_signs ideal model delta sigma weight residual False -2.37 -2.53 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 110 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 111 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 110 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 111 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO G 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " 0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8998 2.85 - 3.36: 20696 3.36 - 3.88: 38997 3.88 - 4.39: 47592 4.39 - 4.90: 82099 Nonbonded interactions: 198382 Sorted by model distance: nonbonded pdb=" O TRP F 74 " pdb=" OG1 THR F 78 " model vdw 2.340 3.040 nonbonded pdb=" O TRP C 74 " pdb=" OG1 THR C 78 " model vdw 2.358 3.040 nonbonded pdb=" O TRP B 74 " pdb=" OG1 THR B 78 " model vdw 2.369 3.040 nonbonded pdb=" O TRP E 74 " pdb=" OG1 THR E 78 " model vdw 2.369 3.040 nonbonded pdb=" O TRP I 74 " pdb=" OG1 THR I 78 " model vdw 2.373 3.040 ... (remaining 198377 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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 individual isotropic 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 27335 Z= 0.350 Angle : 1.138 10.702 36839 Z= 0.476 Chirality : 0.044 0.155 3916 Planarity : 0.007 0.072 4499 Dihedral : 15.908 75.548 9900 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.13 (0.08), residues: 3146 helix: -4.95 (0.03), residues: 2398 sheet: None (None), residues: 0 loop : -2.69 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 240 TYR 0.017 0.002 TYR H 125 PHE 0.013 0.001 PHE E 68 TRP 0.010 0.001 TRP I 262 HIS 0.006 0.001 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.35 (27302) covalent geometry : angle 1.13775 / 0.48 (36773) SS BOND : bond 0.00382 / 0.25 ( 33) SS BOND : angle 1.30269 / 0.82 ( 66) hydrogen bonds : bond 0.37823 / 24.26 ( 1120) hydrogen bonds : angle 11.23706 / 7.67 ( 3267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 1.018 Fit side-chains REVERT: A 88 PHE cc_start: 0.7292 (m-80) cc_final: 0.6952 (m-80) REVERT: A 220 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7777 (tp40) REVERT: A 272 HIS cc_start: 0.7990 (m90) cc_final: 0.7738 (m-70) REVERT: B 88 PHE cc_start: 0.7341 (m-80) cc_final: 0.7105 (m-80) REVERT: B 163 MET cc_start: 0.7893 (ttp) cc_final: 0.7484 (ttm) REVERT: B 176 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 233 TYR cc_start: 0.8864 (m-80) cc_final: 0.8448 (m-80) REVERT: B 273 GLN cc_start: 0.7562 (pt0) cc_final: 0.7225 (pt0) REVERT: C 23 MET cc_start: 0.7937 (ttm) cc_final: 0.7667 (ttp) REVERT: C 31 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 88 PHE cc_start: 0.7495 (m-80) cc_final: 0.6975 (m-80) REVERT: C 243 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7936 (mttt) REVERT: D 31 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 243 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8100 (mttt) REVERT: D 283 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7997 (ttp80) REVERT: E 31 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 32 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7721 (mmm-85) REVERT: E 48 MET cc_start: 0.8101 (tpp) cc_final: 0.7700 (tpt) REVERT: E 176 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7228 (tm-30) REVERT: E 178 GLN cc_start: 0.8769 (mt0) cc_final: 0.8544 (mt0) REVERT: E 273 GLN cc_start: 0.7752 (pt0) cc_final: 0.7519 (pt0) REVERT: F 23 MET cc_start: 0.7937 (ttm) cc_final: 0.7697 (ttp) REVERT: F 31 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 88 PHE cc_start: 0.7290 (m-80) cc_final: 0.6949 (m-80) REVERT: F 163 MET cc_start: 0.7991 (ttp) cc_final: 0.7769 (ttm) REVERT: F 232 ASP cc_start: 0.7822 (t70) cc_final: 0.7618 (t0) REVERT: G 88 PHE cc_start: 0.7097 (m-80) cc_final: 0.6753 (m-80) REVERT: G 176 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7316 (tm-30) REVERT: G 209 TYR cc_start: 0.8075 (t80) cc_final: 0.7852 (t80) REVERT: G 243 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8106 (mttt) REVERT: H 23 MET cc_start: 0.8048 (ttm) cc_final: 0.7818 (ttp) REVERT: H 32 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7627 (mmm-85) REVERT: H 88 PHE cc_start: 0.7120 (m-80) cc_final: 0.6789 (m-80) REVERT: H 176 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7266 (tm-30) REVERT: H 243 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7912 (mttt) REVERT: H 273 GLN cc_start: 0.7473 (pt0) cc_final: 0.7190 (pt0) REVERT: H 283 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8126 (ttp80) REVERT: I 23 MET cc_start: 0.8082 (ttm) cc_final: 0.7802 (ttm) REVERT: I 31 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7316 (tm-30) REVERT: I 88 PHE cc_start: 0.7334 (m-80) cc_final: 0.6817 (m-80) REVERT: I 209 TYR cc_start: 0.7942 (t80) cc_final: 0.7716 (t80) REVERT: I 243 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8006 (mtmm) REVERT: I 273 GLN cc_start: 0.7602 (pt0) cc_final: 0.7395 (pt0) REVERT: J 31 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7595 (tm-30) REVERT: J 88 PHE cc_start: 0.7244 (m-80) cc_final: 0.6829 (m-80) REVERT: J 220 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7729 (tp40) REVERT: J 243 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8032 (mttt) REVERT: J 273 GLN cc_start: 0.7773 (pt0) cc_final: 0.7507 (mt0) REVERT: K 31 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7516 (tm-30) REVERT: K 88 PHE cc_start: 0.7327 (m-80) cc_final: 0.6914 (m-80) REVERT: K 176 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7484 (tm-30) REVERT: K 209 TYR cc_start: 0.8144 (t80) cc_final: 0.7907 (t80) REVERT: K 243 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8077 (mtmm) outliers start: 0 outliers final: 2 residues processed: 640 average time/residue: 0.8572 time to fit residues: 614.8518 Evaluate side-chains 409 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 407 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain D residue 273 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 168 ASN B 228 ASN B 287 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 287 ASN D 47 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 287 ASN E 14 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 273 GLN F 287 ASN G 47 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN G 276 GLN G 287 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN I 47 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN K 178 GLN K 228 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109366 restraints weight = 29492.523| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.14 r_work: 0.3078 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27335 Z= 0.120 Angle : 0.571 14.936 36839 Z= 0.295 Chirality : 0.037 0.159 3916 Planarity : 0.006 0.050 4499 Dihedral : 9.441 72.748 3988 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.29 % Allowed : 13.21 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.12), residues: 3146 helix: -2.84 (0.08), residues: 2255 sheet: None (None), residues: 0 loop : -2.19 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 283 TYR 0.008 0.001 TYR J 278 PHE 0.012 0.001 PHE C 214 TRP 0.015 0.001 TRP G 60 HIS 0.002 0.000 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (27302) covalent geometry : angle 0.57063 / 0.29 (36773) SS BOND : bond 0.00252 / 0.16 ( 33) SS BOND : angle 0.88543 / 0.56 ( 66) hydrogen bonds : bond 0.06430 / 4.15 ( 1120) hydrogen bonds : angle 4.36238 / 2.97 ( 3267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 418 time to evaluate : 1.037 Fit side-chains REVERT: A 85 ARG cc_start: 0.7064 (tpt170) cc_final: 0.6777 (tpt170) REVERT: A 176 GLN cc_start: 0.8200 (tt0) cc_final: 0.7669 (tp40) REVERT: B 22 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: B 23 MET cc_start: 0.7270 (ttm) cc_final: 0.6985 (ttp) REVERT: B 176 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 273 GLN cc_start: 0.7588 (pt0) cc_final: 0.7187 (pt0) REVERT: C 22 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: C 243 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7938 (mttt) REVERT: D 25 LEU cc_start: 0.7853 (tt) cc_final: 0.7578 (tp) REVERT: D 85 ARG cc_start: 0.7046 (tpt170) cc_final: 0.6795 (tpt170) REVERT: D 243 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7862 (mttt) REVERT: E 22 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7242 (m-80) REVERT: E 31 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7445 (tm-30) REVERT: E 32 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7406 (mmm-85) REVERT: E 147 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7959 (tppt) REVERT: E 176 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7388 (tm-30) REVERT: E 273 GLN cc_start: 0.7744 (pt0) cc_final: 0.7442 (pt0) REVERT: F 23 MET cc_start: 0.7613 (ttm) cc_final: 0.7331 (ttp) REVERT: F 88 PHE cc_start: 0.6592 (m-80) cc_final: 0.6337 (m-80) REVERT: F 232 ASP cc_start: 0.8208 (t70) cc_final: 0.7987 (t0) REVERT: G 22 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: G 176 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7406 (tm-30) REVERT: G 209 TYR cc_start: 0.7924 (t80) cc_final: 0.7657 (t80) REVERT: G 243 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8051 (mttt) REVERT: H 23 MET cc_start: 0.7906 (ttm) cc_final: 0.7614 (ttm) REVERT: H 176 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7393 (tm-30) REVERT: H 243 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7670 (mttt) REVERT: H 273 GLN cc_start: 0.7429 (pt0) cc_final: 0.7080 (pt0) REVERT: I 22 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: I 23 MET cc_start: 0.7885 (ttm) cc_final: 0.7638 (ttm) REVERT: I 31 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7422 (tm-30) REVERT: I 133 ARG cc_start: 0.8301 (mmp-170) cc_final: 0.8037 (mmp-170) REVERT: I 243 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7916 (mttt) REVERT: J 85 ARG cc_start: 0.7131 (tpt170) cc_final: 0.6911 (tpt170) REVERT: J 88 PHE cc_start: 0.6642 (m-80) cc_final: 0.6340 (m-80) REVERT: J 129 MET cc_start: 0.8926 (tpp) cc_final: 0.8720 (tpt) REVERT: J 220 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7949 (tp40) REVERT: J 273 GLN cc_start: 0.7778 (pt0) cc_final: 0.7559 (mt0) REVERT: K 11 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: K 113 MET cc_start: 0.8615 (mtp) cc_final: 0.8365 (mtp) REVERT: K 176 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7624 (tm-30) REVERT: K 243 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8123 (mtmm) outliers start: 64 outliers final: 18 residues processed: 452 average time/residue: 0.7522 time to fit residues: 386.6993 Evaluate side-chains 400 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 376 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 10.0000 chunk 277 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 47 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107736 restraints weight = 29610.092| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.13 r_work: 0.3054 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27335 Z= 0.124 Angle : 0.558 19.328 36839 Z= 0.277 Chirality : 0.038 0.174 3916 Planarity : 0.004 0.040 4499 Dihedral : 8.837 59.856 3982 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.01 % Allowed : 14.64 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 3146 helix: -1.49 (0.10), residues: 2321 sheet: None (None), residues: 0 loop : -1.73 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 283 TYR 0.010 0.001 TYR D 278 PHE 0.014 0.001 PHE H 88 TRP 0.012 0.001 TRP I 150 HIS 0.002 0.000 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (27302) covalent geometry : angle 0.55674 / 0.28 (36773) SS BOND : bond 0.00321 / 0.20 ( 33) SS BOND : angle 0.93746 / 0.60 ( 66) hydrogen bonds : bond 0.05627 / 3.65 ( 1120) hydrogen bonds : angle 3.63337 / 2.49 ( 3267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 399 time to evaluate : 1.073 Fit side-chains REVERT: A 85 ARG cc_start: 0.7247 (tpt170) cc_final: 0.6978 (tpt170) REVERT: A 176 GLN cc_start: 0.8117 (tt0) cc_final: 0.7654 (tp40) REVERT: B 85 ARG cc_start: 0.7155 (tpt170) cc_final: 0.6952 (tpt170) REVERT: B 176 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 273 GLN cc_start: 0.7562 (pt0) cc_final: 0.7172 (pt0) REVERT: C 22 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: C 26 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 85 ARG cc_start: 0.7068 (tpt170) cc_final: 0.6799 (tpt170) REVERT: C 88 PHE cc_start: 0.7003 (m-80) cc_final: 0.6797 (m-80) REVERT: C 243 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7904 (mttt) REVERT: D 25 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7577 (tp) REVERT: D 129 MET cc_start: 0.8910 (tpt) cc_final: 0.8208 (tpt) REVERT: D 133 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.7984 (mmp80) REVERT: D 243 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7908 (mttt) REVERT: E 22 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: E 25 LEU cc_start: 0.7990 (tt) cc_final: 0.7789 (tp) REVERT: E 32 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7399 (mmm-85) REVERT: E 44 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8492 (p) REVERT: E 85 ARG cc_start: 0.7246 (mmm160) cc_final: 0.7017 (tpt170) REVERT: E 176 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 227 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7629 (mp0) REVERT: E 273 GLN cc_start: 0.7795 (pt0) cc_final: 0.7509 (pt0) REVERT: F 31 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7804 (tm-30) REVERT: F 232 ASP cc_start: 0.8240 (t70) cc_final: 0.8030 (t0) REVERT: G 22 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: G 176 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7361 (tm-30) REVERT: G 209 TYR cc_start: 0.8056 (t80) cc_final: 0.7816 (t80) REVERT: H 25 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7552 (tp) REVERT: H 32 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7659 (mmm-85) REVERT: H 176 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7422 (tm-30) REVERT: H 243 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7668 (mttt) REVERT: H 273 GLN cc_start: 0.7447 (pt0) cc_final: 0.7149 (pt0) REVERT: I 22 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: I 23 MET cc_start: 0.7805 (ttm) cc_final: 0.7537 (ttm) REVERT: I 31 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7417 (tm-30) REVERT: I 85 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6908 (tpt170) REVERT: I 133 ARG cc_start: 0.8314 (mmp-170) cc_final: 0.8016 (mmp-170) REVERT: I 243 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7911 (mttt) REVERT: J 85 ARG cc_start: 0.7105 (tpt170) cc_final: 0.6860 (tpt170) REVERT: J 88 PHE cc_start: 0.6967 (m-80) cc_final: 0.6703 (m-80) REVERT: J 133 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7999 (mmp80) REVERT: J 220 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7964 (tp40) REVERT: J 273 GLN cc_start: 0.7788 (pt0) cc_final: 0.7574 (mt0) REVERT: K 11 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6553 (m-10) REVERT: K 48 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (tpt) REVERT: K 113 MET cc_start: 0.8543 (mtp) cc_final: 0.8325 (mtp) REVERT: K 176 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7489 (tm-30) REVERT: K 243 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8089 (mtmm) outliers start: 84 outliers final: 38 residues processed: 457 average time/residue: 0.7465 time to fit residues: 388.0326 Evaluate side-chains 447 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 399 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 65 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 290 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.105565 restraints weight = 29425.586| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.10 r_work: 0.3015 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27335 Z= 0.165 Angle : 0.591 16.409 36839 Z= 0.292 Chirality : 0.041 0.170 3916 Planarity : 0.004 0.037 4499 Dihedral : 8.995 59.854 3982 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.44 % Allowed : 15.71 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 3146 helix: -1.00 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 283 TYR 0.011 0.001 TYR C 278 PHE 0.012 0.001 PHE F 88 TRP 0.013 0.002 TRP I 150 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (27302) covalent geometry : angle 0.58921 / 0.29 (36773) SS BOND : bond 0.00467 / 0.30 ( 33) SS BOND : angle 1.23527 / 0.79 ( 66) hydrogen bonds : bond 0.06112 / 3.96 ( 1120) hydrogen bonds : angle 3.53612 / 2.43 ( 3267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 406 time to evaluate : 1.016 Fit side-chains REVERT: A 88 PHE cc_start: 0.7236 (m-80) cc_final: 0.6937 (m-80) REVERT: A 151 GLU cc_start: 0.7902 (mp0) cc_final: 0.7654 (mt-10) REVERT: B 85 ARG cc_start: 0.7149 (tpt170) cc_final: 0.6922 (tpt170) REVERT: B 176 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 22 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7242 (m-80) REVERT: C 26 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 85 ARG cc_start: 0.7056 (tpt170) cc_final: 0.6705 (tpt170) REVERT: C 88 PHE cc_start: 0.7033 (m-80) cc_final: 0.6804 (m-80) REVERT: C 243 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7988 (mttt) REVERT: D 85 ARG cc_start: 0.7193 (tpt170) cc_final: 0.6183 (tpt170) REVERT: D 133 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.8104 (mmp80) REVERT: D 243 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7965 (mttt) REVERT: D 283 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8211 (ttp80) REVERT: E 32 ARG cc_start: 0.7599 (mmm160) cc_final: 0.7301 (mmm-85) REVERT: E 85 ARG cc_start: 0.7105 (mmm160) cc_final: 0.6534 (tpt170) REVERT: E 88 PHE cc_start: 0.7225 (m-80) cc_final: 0.6576 (m-80) REVERT: E 176 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7714 (tm-30) REVERT: E 273 GLN cc_start: 0.7631 (pt0) cc_final: 0.7299 (pt0) REVERT: F 88 PHE cc_start: 0.6916 (m-80) cc_final: 0.6697 (m-80) REVERT: F 232 ASP cc_start: 0.8449 (t70) cc_final: 0.8243 (t0) REVERT: G 22 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7217 (m-80) REVERT: G 176 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7563 (tm-30) REVERT: H 25 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7398 (tp) REVERT: H 32 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7629 (mmm-85) REVERT: H 133 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8119 (mmp80) REVERT: H 176 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7570 (tm-30) REVERT: H 243 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7735 (mttt) REVERT: H 273 GLN cc_start: 0.7371 (pt0) cc_final: 0.7086 (pt0) REVERT: I 22 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: I 23 MET cc_start: 0.7629 (ttm) cc_final: 0.7355 (ttm) REVERT: I 31 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7639 (tm-30) REVERT: I 85 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6845 (tpt170) REVERT: I 243 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7959 (mttt) REVERT: J 85 ARG cc_start: 0.7068 (tpt170) cc_final: 0.6806 (tpt170) REVERT: J 88 PHE cc_start: 0.6868 (m-80) cc_final: 0.6663 (m-80) REVERT: J 133 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8059 (mmp80) REVERT: J 140 LEU cc_start: 0.8326 (mt) cc_final: 0.8065 (mt) REVERT: J 220 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8219 (tp40) REVERT: K 11 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6464 (m-10) REVERT: K 113 MET cc_start: 0.8791 (mtp) cc_final: 0.8552 (mtm) REVERT: K 148 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: K 176 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7673 (tm-30) REVERT: K 243 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8158 (mtmm) outliers start: 96 outliers final: 56 residues processed: 465 average time/residue: 0.7054 time to fit residues: 372.9586 Evaluate side-chains 473 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 410 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 273 GLN Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 294 optimal weight: 0.0020 chunk 184 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 196 optimal weight: 0.0370 chunk 212 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN F 47 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111096 restraints weight = 29416.430| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.12 r_work: 0.3104 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27335 Z= 0.091 Angle : 0.496 15.808 36839 Z= 0.246 Chirality : 0.036 0.172 3916 Planarity : 0.003 0.035 4499 Dihedral : 8.215 59.495 3982 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.51 % Allowed : 17.36 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3146 helix: -0.20 (0.11), residues: 2255 sheet: None (None), residues: 0 loop : -1.53 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.008 0.001 TYR J 278 PHE 0.019 0.001 PHE G 88 TRP 0.013 0.001 TRP I 150 HIS 0.002 0.000 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (27302) covalent geometry : angle 0.49561 / 0.25 (36773) SS BOND : bond 0.00145 / 0.09 ( 33) SS BOND : angle 0.65984 / 0.44 ( 66) hydrogen bonds : bond 0.03778 / 2.45 ( 1120) hydrogen bonds : angle 3.23347 / 2.21 ( 3267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 392 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7862 (tpm-80) cc_final: 0.7583 (tpm-80) REVERT: A 68 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7271 (t80) REVERT: A 151 GLU cc_start: 0.7754 (mp0) cc_final: 0.7525 (mt-10) REVERT: A 176 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: B 22 PHE cc_start: 0.7595 (t80) cc_final: 0.7292 (t80) REVERT: B 133 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.7931 (mmp80) REVERT: B 176 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 85 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6717 (tpt170) REVERT: C 88 PHE cc_start: 0.7165 (m-80) cc_final: 0.6880 (m-80) REVERT: C 243 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7836 (mttt) REVERT: D 95 ARG cc_start: 0.7187 (ttt90) cc_final: 0.6939 (ttt90) REVERT: D 133 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8130 (mmp80) REVERT: D 202 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7890 (mmt180) REVERT: D 283 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8082 (ttp80) REVERT: E 34 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7241 (t80) REVERT: E 176 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7441 (tm-30) REVERT: E 227 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7600 (mp0) REVERT: E 273 GLN cc_start: 0.7677 (pt0) cc_final: 0.7350 (pt0) REVERT: F 85 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6722 (tpt170) REVERT: F 232 ASP cc_start: 0.8270 (t70) cc_final: 0.8063 (t0) REVERT: G 68 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7412 (t80) REVERT: G 176 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7426 (tm-30) REVERT: H 25 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7464 (tp) REVERT: H 133 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8065 (mmp80) REVERT: H 176 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7482 (tm-30) REVERT: H 243 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7606 (mttt) REVERT: H 273 GLN cc_start: 0.7391 (pt0) cc_final: 0.7165 (pt0) REVERT: I 23 MET cc_start: 0.7354 (ttm) cc_final: 0.7120 (ttm) REVERT: I 31 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7473 (tm-30) REVERT: I 85 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6967 (tpt170) REVERT: I 133 ARG cc_start: 0.8208 (mmp-170) cc_final: 0.7822 (mmp-170) REVERT: I 147 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7671 (tppt) REVERT: I 243 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7854 (mttt) REVERT: J 68 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7255 (t80) REVERT: J 140 LEU cc_start: 0.8316 (mt) cc_final: 0.8113 (mt) REVERT: J 220 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7822 (tp40) REVERT: K 11 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6454 (m-10) REVERT: K 68 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7414 (t80) REVERT: K 148 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: K 176 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7456 (tm-30) REVERT: K 243 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7975 (mttt) outliers start: 70 outliers final: 24 residues processed: 431 average time/residue: 0.7277 time to fit residues: 357.0268 Evaluate side-chains 415 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 279 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 263 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109191 restraints weight = 29636.294| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.09 r_work: 0.3072 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27335 Z= 0.107 Angle : 0.513 15.377 36839 Z= 0.253 Chirality : 0.038 0.166 3916 Planarity : 0.003 0.033 4499 Dihedral : 8.163 59.993 3982 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.43 % Allowed : 18.25 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3146 helix: -0.01 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.32 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 95 TYR 0.009 0.001 TYR F 278 PHE 0.023 0.001 PHE A 88 TRP 0.014 0.001 TRP I 150 HIS 0.002 0.000 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (27302) covalent geometry : angle 0.51180 / 0.25 (36773) SS BOND : bond 0.00269 / 0.17 ( 33) SS BOND : angle 0.84579 / 0.55 ( 66) hydrogen bonds : bond 0.04551 / 2.95 ( 1120) hydrogen bonds : angle 3.15642 / 2.16 ( 3267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 394 time to evaluate : 1.021 Fit side-chains REVERT: A 151 GLU cc_start: 0.7832 (mp0) cc_final: 0.7564 (mt-10) REVERT: A 176 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: B 22 PHE cc_start: 0.7542 (t80) cc_final: 0.7224 (t80) REVERT: B 133 ARG cc_start: 0.8486 (tpp-160) cc_final: 0.8021 (mmp80) REVERT: B 176 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 273 GLN cc_start: 0.7734 (pt0) cc_final: 0.7438 (pt0) REVERT: C 85 ARG cc_start: 0.6896 (tpt170) cc_final: 0.6518 (tpt170) REVERT: C 88 PHE cc_start: 0.6914 (m-80) cc_final: 0.6638 (m-80) REVERT: C 243 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8000 (mttt) REVERT: D 85 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6045 (tpt170) REVERT: D 133 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8106 (mmp80) REVERT: D 283 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8174 (ttp80) REVERT: E 11 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.6127 (m-10) REVERT: E 85 ARG cc_start: 0.7158 (mmm160) cc_final: 0.6635 (tpt170) REVERT: E 88 PHE cc_start: 0.7076 (m-80) cc_final: 0.6446 (m-80) REVERT: E 176 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7713 (tm-30) REVERT: E 204 ARG cc_start: 0.8312 (mmm160) cc_final: 0.8014 (mmm160) REVERT: E 227 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7752 (mp0) REVERT: E 273 GLN cc_start: 0.7584 (pt0) cc_final: 0.7224 (pt0) REVERT: F 88 PHE cc_start: 0.7125 (m-80) cc_final: 0.6764 (m-80) REVERT: G 68 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7525 (t80) REVERT: G 176 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7616 (tm-30) REVERT: H 25 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7428 (tp) REVERT: H 32 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7654 (mmm-85) REVERT: H 68 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7513 (t80) REVERT: H 133 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8188 (mmp80) REVERT: H 176 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7708 (tm-30) REVERT: H 220 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8124 (tp40) REVERT: H 224 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7900 (pt0) REVERT: H 243 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7749 (mttt) REVERT: H 273 GLN cc_start: 0.7336 (pt0) cc_final: 0.7107 (pt0) REVERT: I 31 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7697 (tm-30) REVERT: I 85 ARG cc_start: 0.7265 (tpt170) cc_final: 0.6941 (tpt170) REVERT: I 133 ARG cc_start: 0.8285 (mmp-170) cc_final: 0.7951 (mmp-170) REVERT: I 243 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7979 (mttt) REVERT: J 220 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8131 (tp40) REVERT: K 11 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: K 148 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: K 176 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7664 (tm-30) REVERT: K 243 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8098 (mttt) outliers start: 68 outliers final: 34 residues processed: 433 average time/residue: 0.7507 time to fit residues: 368.3666 Evaluate side-chains 420 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 34 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 140 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 280 optimal weight: 0.1980 chunk 290 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 222 optimal weight: 0.0170 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN K 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107666 restraints weight = 29479.367| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.09 r_work: 0.3047 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27335 Z= 0.127 Angle : 0.534 14.302 36839 Z= 0.265 Chirality : 0.039 0.165 3916 Planarity : 0.003 0.033 4499 Dihedral : 8.266 58.851 3982 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.79 % Allowed : 18.47 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3146 helix: 0.14 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.24 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.010 0.001 TYR F 278 PHE 0.023 0.001 PHE A 88 TRP 0.017 0.001 TRP I 150 HIS 0.002 0.000 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (27302) covalent geometry : angle 0.53321 / 0.26 (36773) SS BOND : bond 0.00346 / 0.22 ( 33) SS BOND : angle 0.99715 / 0.64 ( 66) hydrogen bonds : bond 0.05057 / 3.28 ( 1120) hydrogen bonds : angle 3.19713 / 2.19 ( 3267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 395 time to evaluate : 0.911 Fit side-chains REVERT: A 151 GLU cc_start: 0.7817 (mp0) cc_final: 0.7555 (mt-10) REVERT: B 22 PHE cc_start: 0.7562 (t80) cc_final: 0.7267 (t80) REVERT: B 133 ARG cc_start: 0.8512 (tpp-160) cc_final: 0.7986 (mmp80) REVERT: B 176 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 273 GLN cc_start: 0.7735 (pt0) cc_final: 0.7452 (pt0) REVERT: C 85 ARG cc_start: 0.6878 (tpt170) cc_final: 0.6498 (tpt170) REVERT: C 88 PHE cc_start: 0.7040 (m-80) cc_final: 0.6746 (m-80) REVERT: C 243 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8007 (mttt) REVERT: D 85 ARG cc_start: 0.7156 (tpt170) cc_final: 0.6920 (tpt170) REVERT: D 133 ARG cc_start: 0.8437 (tpp-160) cc_final: 0.8102 (mmp80) REVERT: D 148 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: D 283 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8177 (ttp80) REVERT: E 11 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: E 44 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8637 (p) REVERT: E 85 ARG cc_start: 0.7160 (mmm160) cc_final: 0.6888 (tpt170) REVERT: E 176 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 204 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8131 (mmm160) REVERT: E 273 GLN cc_start: 0.7548 (pt0) cc_final: 0.7245 (pt0) REVERT: G 68 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7575 (t80) REVERT: G 176 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 25 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7306 (tp) REVERT: H 68 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7450 (t80) REVERT: H 133 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8161 (mmp80) REVERT: H 176 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7725 (tm-30) REVERT: H 243 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7787 (mttt) REVERT: H 273 GLN cc_start: 0.7324 (pt0) cc_final: 0.7090 (pt0) REVERT: I 31 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7747 (tm-30) REVERT: I 85 ARG cc_start: 0.7275 (tpt170) cc_final: 0.6965 (tpt170) REVERT: I 133 ARG cc_start: 0.8319 (mmp-170) cc_final: 0.8028 (mmp-170) REVERT: I 243 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7995 (mttt) REVERT: J 68 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7484 (t80) REVERT: J 147 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7844 (tptt) REVERT: J 220 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8150 (tp40) REVERT: K 11 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6350 (m-10) REVERT: K 68 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7608 (t80) REVERT: K 148 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: K 176 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7726 (tm-30) REVERT: K 243 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8154 (mtmm) outliers start: 78 outliers final: 47 residues processed: 444 average time/residue: 0.7164 time to fit residues: 361.7901 Evaluate side-chains 446 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 389 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 158 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 204 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 155 optimal weight: 0.4980 chunk 143 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 194 optimal weight: 0.0570 chunk 201 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 248 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 225 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN K 273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109239 restraints weight = 29703.036| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.10 r_work: 0.3073 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27335 Z= 0.102 Angle : 0.502 13.275 36839 Z= 0.251 Chirality : 0.037 0.155 3916 Planarity : 0.003 0.033 4499 Dihedral : 8.008 58.690 3982 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.61 % Allowed : 19.18 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 3146 helix: 0.45 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.22 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.008 0.001 TYR D 278 PHE 0.025 0.001 PHE A 88 TRP 0.017 0.001 TRP I 150 HIS 0.002 0.000 HIS G 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (27302) covalent geometry : angle 0.50175 / 0.25 (36773) SS BOND : bond 0.00233 / 0.15 ( 33) SS BOND : angle 0.81316 / 0.53 ( 66) hydrogen bonds : bond 0.04335 / 2.81 ( 1120) hydrogen bonds : angle 3.11013 / 2.13 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 384 time to evaluate : 0.972 Fit side-chains REVERT: A 151 GLU cc_start: 0.7816 (mp0) cc_final: 0.7550 (mt-10) REVERT: A 176 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7621 (tp40) REVERT: B 22 PHE cc_start: 0.7584 (t80) cc_final: 0.7266 (t80) REVERT: B 176 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7529 (tm-30) REVERT: C 31 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 85 ARG cc_start: 0.6769 (tpt170) cc_final: 0.6403 (tpt170) REVERT: C 88 PHE cc_start: 0.6756 (m-80) cc_final: 0.6474 (m-80) REVERT: C 243 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7981 (mttt) REVERT: D 85 ARG cc_start: 0.7150 (tpt170) cc_final: 0.5970 (tpt170) REVERT: D 133 ARG cc_start: 0.8515 (tpp-160) cc_final: 0.8114 (mmp80) REVERT: D 148 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: D 283 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8190 (ttp80) REVERT: E 11 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: E 31 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 34 PHE cc_start: 0.8070 (m-80) cc_final: 0.7128 (t80) REVERT: E 44 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8594 (p) REVERT: E 176 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7736 (tm-30) REVERT: E 204 ARG cc_start: 0.8281 (mmm160) cc_final: 0.8007 (mmm160) REVERT: E 273 GLN cc_start: 0.7536 (pt0) cc_final: 0.7246 (pt0) REVERT: F 85 ARG cc_start: 0.6833 (tpt170) cc_final: 0.6600 (tpt170) REVERT: G 68 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7535 (t80) REVERT: G 176 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7616 (tm-30) REVERT: H 25 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7304 (tp) REVERT: H 68 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7431 (t80) REVERT: H 133 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8227 (mmp80) REVERT: H 176 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7693 (tm-30) REVERT: H 243 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7672 (mttt) REVERT: H 273 GLN cc_start: 0.7337 (pt0) cc_final: 0.7114 (pt0) REVERT: I 31 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7712 (tm-30) REVERT: I 85 ARG cc_start: 0.7347 (tpt170) cc_final: 0.7034 (tpt170) REVERT: I 243 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7989 (mttt) REVERT: J 68 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7425 (t80) REVERT: J 85 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6769 (tpt170) REVERT: J 88 PHE cc_start: 0.6911 (m-80) cc_final: 0.6572 (m-80) REVERT: J 220 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8059 (tp40) REVERT: K 11 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.6142 (m-10) REVERT: K 88 PHE cc_start: 0.7098 (m-80) cc_final: 0.6842 (m-80) REVERT: K 148 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: K 176 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7718 (tm-30) REVERT: K 243 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8145 (mtmm) outliers start: 73 outliers final: 41 residues processed: 431 average time/residue: 0.7682 time to fit residues: 375.9011 Evaluate side-chains 425 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 374 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 158 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 204 optimal weight: 0.0670 chunk 230 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108474 restraints weight = 29588.772| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.09 r_work: 0.3053 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27335 Z= 0.113 Angle : 0.516 13.138 36839 Z= 0.258 Chirality : 0.038 0.149 3916 Planarity : 0.003 0.037 4499 Dihedral : 8.003 58.921 3982 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.58 % Allowed : 19.51 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 3146 helix: 0.58 (0.11), residues: 2321 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 283 TYR 0.009 0.001 TYR C 278 PHE 0.027 0.001 PHE F 88 TRP 0.019 0.001 TRP I 150 HIS 0.002 0.000 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (27302) covalent geometry : angle 0.51487 / 0.26 (36773) SS BOND : bond 0.00292 / 0.18 ( 33) SS BOND : angle 0.89319 / 0.57 ( 66) hydrogen bonds : bond 0.04665 / 3.03 ( 1120) hydrogen bonds : angle 3.11706 / 2.14 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 381 time to evaluate : 0.922 Fit side-chains REVERT: A 151 GLU cc_start: 0.7830 (mp0) cc_final: 0.7564 (mt-10) REVERT: B 22 PHE cc_start: 0.7599 (t80) cc_final: 0.7286 (t80) REVERT: B 176 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 31 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 85 ARG cc_start: 0.6818 (tpt170) cc_final: 0.6454 (tpt170) REVERT: C 88 PHE cc_start: 0.6777 (m-80) cc_final: 0.6484 (m-80) REVERT: C 243 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7968 (mttt) REVERT: D 85 ARG cc_start: 0.7188 (tpt170) cc_final: 0.6008 (tpt170) REVERT: D 133 ARG cc_start: 0.8540 (tpp-160) cc_final: 0.8109 (mmp80) REVERT: E 11 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.6166 (m-10) REVERT: E 34 PHE cc_start: 0.8038 (m-80) cc_final: 0.7122 (t80) REVERT: E 44 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8632 (p) REVERT: E 176 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7715 (tm-30) REVERT: E 204 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8111 (mmm160) REVERT: E 273 GLN cc_start: 0.7531 (pt0) cc_final: 0.7243 (pt0) REVERT: F 85 ARG cc_start: 0.6908 (tpt170) cc_final: 0.6644 (tpt170) REVERT: G 68 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7554 (t80) REVERT: G 176 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7628 (tm-30) REVERT: H 25 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7267 (tp) REVERT: H 68 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7445 (t80) REVERT: H 133 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8169 (mmp80) REVERT: H 176 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7737 (tm-30) REVERT: H 243 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7711 (mttt) REVERT: H 273 GLN cc_start: 0.7306 (pt0) cc_final: 0.7080 (pt0) REVERT: I 31 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7718 (tm-30) REVERT: I 85 ARG cc_start: 0.7260 (tpt170) cc_final: 0.6948 (tpt170) REVERT: I 243 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7951 (mttt) REVERT: J 68 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7453 (t80) REVERT: J 85 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6749 (tpt170) REVERT: J 88 PHE cc_start: 0.7009 (m-80) cc_final: 0.6670 (m-80) REVERT: J 148 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6600 (pm20) REVERT: J 220 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8042 (tp40) REVERT: J 275 GLN cc_start: 0.7109 (pm20) cc_final: 0.6895 (pm20) REVERT: K 11 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6137 (m-10) REVERT: K 88 PHE cc_start: 0.7098 (m-80) cc_final: 0.6867 (m-80) REVERT: K 148 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: K 176 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7730 (tm-30) REVERT: K 243 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8151 (mtmm) outliers start: 72 outliers final: 47 residues processed: 426 average time/residue: 0.7555 time to fit residues: 365.8255 Evaluate side-chains 433 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 377 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 158 CYS Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 203 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 248 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109223 restraints weight = 29552.416| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.09 r_work: 0.3064 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27335 Z= 0.107 Angle : 0.510 13.045 36839 Z= 0.255 Chirality : 0.038 0.150 3916 Planarity : 0.003 0.039 4499 Dihedral : 7.906 58.892 3982 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.11 % Allowed : 20.08 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 3146 helix: 0.86 (0.12), residues: 2266 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 283 TYR 0.008 0.001 TYR J 278 PHE 0.026 0.001 PHE F 88 TRP 0.018 0.001 TRP I 150 HIS 0.002 0.000 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (27302) covalent geometry : angle 0.50923 / 0.25 (36773) SS BOND : bond 0.00251 / 0.16 ( 33) SS BOND : angle 0.82829 / 0.53 ( 66) hydrogen bonds : bond 0.04422 / 2.87 ( 1120) hydrogen bonds : angle 3.09444 / 2.12 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 379 time to evaluate : 1.034 Fit side-chains REVERT: A 151 GLU cc_start: 0.7830 (mp0) cc_final: 0.7557 (mt-10) REVERT: A 176 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7609 (tp40) REVERT: B 22 PHE cc_start: 0.7570 (t80) cc_final: 0.7268 (t80) REVERT: B 176 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 31 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 85 ARG cc_start: 0.6777 (tpt170) cc_final: 0.6409 (tpt170) REVERT: C 88 PHE cc_start: 0.6720 (m-80) cc_final: 0.6436 (m-80) REVERT: C 243 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7986 (mttt) REVERT: D 85 ARG cc_start: 0.7192 (tpt170) cc_final: 0.6012 (tpt170) REVERT: D 133 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8085 (mmp80) REVERT: D 176 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7488 (tm-30) REVERT: E 34 PHE cc_start: 0.8020 (m-80) cc_final: 0.7143 (t80) REVERT: E 44 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8602 (p) REVERT: E 176 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 204 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8026 (mmm160) REVERT: E 273 GLN cc_start: 0.7461 (pt0) cc_final: 0.7190 (pt0) REVERT: F 85 ARG cc_start: 0.6899 (tpt170) cc_final: 0.6631 (tpt170) REVERT: G 68 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7579 (t80) REVERT: G 176 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7645 (tm-30) REVERT: H 25 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7285 (tp) REVERT: H 68 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7449 (t80) REVERT: H 133 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8138 (mmp80) REVERT: H 176 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7726 (tm-30) REVERT: H 243 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7701 (mttt) REVERT: H 273 GLN cc_start: 0.7334 (pt0) cc_final: 0.7133 (pt0) REVERT: I 31 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7728 (tm-30) REVERT: I 85 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6936 (tpt170) REVERT: I 243 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7930 (mttt) REVERT: J 68 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7432 (t80) REVERT: J 85 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6652 (tpt170) REVERT: J 88 PHE cc_start: 0.6969 (m-80) cc_final: 0.6634 (m-80) REVERT: J 148 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: J 220 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8038 (tp40) REVERT: K 11 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.6128 (m-10) REVERT: K 148 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: K 176 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7722 (tm-30) REVERT: K 243 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8053 (mttt) outliers start: 59 outliers final: 44 residues processed: 414 average time/residue: 0.7715 time to fit residues: 362.7862 Evaluate side-chains 433 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 158 CYS Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 158 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 192 optimal weight: 0.0980 chunk 306 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 248 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106011 restraints weight = 29583.639| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.08 r_work: 0.3022 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27335 Z= 0.167 Angle : 0.572 13.150 36839 Z= 0.286 Chirality : 0.041 0.146 3916 Planarity : 0.004 0.037 4499 Dihedral : 8.406 59.868 3982 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 20.11 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 3146 helix: 0.45 (0.11), residues: 2343 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 283 TYR 0.011 0.001 TYR C 278 PHE 0.026 0.001 PHE I 88 TRP 0.018 0.002 TRP I 150 HIS 0.003 0.000 HIS J 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (27302) covalent geometry : angle 0.57066 / 0.29 (36773) SS BOND : bond 0.00497 / 0.32 ( 33) SS BOND : angle 1.21433 / 0.77 ( 66) hydrogen bonds : bond 0.05750 / 3.73 ( 1120) hydrogen bonds : angle 3.25857 / 2.24 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10487.87 seconds wall clock time: 193 minutes 59.79 seconds (11639.79 seconds total)