Starting phenix.real_space_refine on Thu Feb 5 00:24:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.map" model { file = "/net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lba_62938/02_2026/9lba_62938.cif" } resolution = 2.85 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9120 2.51 5 N 2025 2.21 5 O 2600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13795 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 231 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 204 Unusual residues: {' CL': 1, 'PEE': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 204 Unusual residues: {' CL': 1, 'PEE': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 204 Unusual residues: {' CL': 1, 'PEE': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 177 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 3.46, per 1000 atoms: 0.25 Number of scatterers: 13795 At special positions: 0 Unit cell: (91.2, 92.72, 128.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 25 15.00 O 2600 8.00 N 2025 7.00 C 9120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 575.6 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 40.7% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.769A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.710A pdb=" N ASN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.625A pdb=" N TRP A 217 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.646A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.769A pdb=" N VAL B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.710A pdb=" N ASN B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.625A pdb=" N TRP B 217 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 218' Processing helix chain 'B' and resid 220 through 244 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 286 through 316 removed outlier: 3.645A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.769A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.710A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.625A pdb=" N TRP C 217 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 218' Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 286 through 316 removed outlier: 3.645A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.770A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.710A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.625A pdb=" N TRP D 217 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 214 through 218' Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 286 through 316 removed outlier: 3.646A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 50 through 53 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.769A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 196 through 213 removed outlier: 3.710A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.625A pdb=" N TRP E 217 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 214 through 218' Processing helix chain 'E' and resid 220 through 244 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 286 through 316 removed outlier: 3.645A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.833A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.833A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 10.917A pdb=" N ARG A 179 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ASN A 173 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 181 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 10.916A pdb=" N ARG B 179 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ASN B 173 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU B 181 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 10.917A pdb=" N ARG C 179 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N ASN C 173 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 10.917A pdb=" N ARG D 179 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N ASN D 173 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU D 181 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.834A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 10.917A pdb=" N ARG E 179 " --> pdb=" O ASN E 173 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ASN E 173 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU E 181 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2075 1.32 - 1.44: 3750 1.44 - 1.56: 8055 1.56 - 1.68: 50 1.68 - 1.81: 35 Bond restraints: 13965 Sorted by residual: bond pdb=" CB LEU D 203 " pdb=" CG LEU D 203 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" CB LEU E 203 " pdb=" CG LEU E 203 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CB LEU B 203 " pdb=" CG LEU B 203 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CB LEU A 203 " pdb=" CG LEU A 203 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" CB LEU C 203 " pdb=" CG LEU C 203 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 13960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 16847 1.14 - 2.29: 1519 2.29 - 3.43: 265 3.43 - 4.57: 158 4.57 - 5.72: 56 Bond angle restraints: 18845 Sorted by residual: angle pdb=" C TYR B 186 " pdb=" N GLN B 187 " pdb=" CA GLN B 187 " ideal model delta sigma weight residual 122.93 117.88 5.05 1.45e+00 4.76e-01 1.21e+01 angle pdb=" C TYR A 186 " pdb=" N GLN A 187 " pdb=" CA GLN A 187 " ideal model delta sigma weight residual 122.93 117.89 5.04 1.45e+00 4.76e-01 1.21e+01 angle pdb=" C TYR E 186 " pdb=" N GLN E 187 " pdb=" CA GLN E 187 " ideal model delta sigma weight residual 122.93 117.89 5.04 1.45e+00 4.76e-01 1.21e+01 angle pdb=" C TYR C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta sigma weight residual 122.93 117.91 5.02 1.45e+00 4.76e-01 1.20e+01 angle pdb=" C TYR D 186 " pdb=" N GLN D 187 " pdb=" CA GLN D 187 " ideal model delta sigma weight residual 122.93 117.91 5.02 1.45e+00 4.76e-01 1.20e+01 ... (remaining 18840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 8060 30.86 - 61.71: 335 61.71 - 92.57: 75 92.57 - 123.42: 25 123.42 - 154.28: 10 Dihedral angle restraints: 8505 sinusoidal: 3825 harmonic: 4680 Sorted by residual: dihedral pdb=" C32 PEE B 407 " pdb=" C30 PEE B 407 " pdb=" C31 PEE B 407 " pdb=" O3 PEE B 407 " ideal model delta sinusoidal sigma weight residual 161.16 -44.56 -154.28 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C32 PEE D 407 " pdb=" C30 PEE D 407 " pdb=" C31 PEE D 407 " pdb=" O3 PEE D 407 " ideal model delta sinusoidal sigma weight residual 161.16 -44.59 -154.25 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C32 PEE C 407 " pdb=" C30 PEE C 407 " pdb=" C31 PEE C 407 " pdb=" O3 PEE C 407 " ideal model delta sinusoidal sigma weight residual 161.16 -44.60 -154.24 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1749 0.073 - 0.147: 291 0.147 - 0.220: 55 0.220 - 0.293: 0 0.293 - 0.367: 5 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CG LEU D 203 " pdb=" CB LEU D 203 " pdb=" CD1 LEU D 203 " pdb=" CD2 LEU D 203 " both_signs ideal model delta sigma weight residual False -2.59 -2.96 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CG LEU C 203 " pdb=" CB LEU C 203 " pdb=" CD1 LEU C 203 " pdb=" CD2 LEU C 203 " both_signs ideal model delta sigma weight residual False -2.59 -2.96 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CG LEU E 203 " pdb=" CB LEU E 203 " pdb=" CD1 LEU E 203 " pdb=" CD2 LEU E 203 " both_signs ideal model delta sigma weight residual False -2.59 -2.96 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 2097 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 139 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" CG ASN E 139 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN E 139 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN E 139 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 139 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" CG ASN A 139 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 139 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 139 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 139 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" CG ASN B 139 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 139 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 139 " 0.027 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4045 2.83 - 3.35: 11391 3.35 - 3.87: 21689 3.87 - 4.38: 25560 4.38 - 4.90: 45421 Nonbonded interactions: 108106 Sorted by model distance: nonbonded pdb=" O LEU B 209 " pdb=" OG SER B 212 " model vdw 2.318 3.040 nonbonded pdb=" O LEU A 209 " pdb=" OG SER A 212 " model vdw 2.319 3.040 nonbonded pdb=" O LEU C 209 " pdb=" OG SER C 212 " model vdw 2.319 3.040 nonbonded pdb=" O LEU D 209 " pdb=" OG SER D 212 " model vdw 2.319 3.040 nonbonded pdb=" O LEU E 209 " pdb=" OG SER E 212 " model vdw 2.319 3.040 ... (remaining 108101 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 316 or (resid 403 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name O1P or name O2 or name O2P or name O3 or name O \ 3P or name O4 or name O4P or name O5 or name P )) or resid 404 or (resid 405 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 16 or name C17 or name C18 or name C19)) or (resid 406 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or (resid 407 and (name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C20 or name C21 or name C22)))) selection = (chain 'B' and (resid 5 through 316 or resid 403 or (resid 404 and (name C1 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or name C3 \ 1 or name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C10 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 17 or name C18 or name C19)) or (resid 406 and (name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22)) or (resid 407 and (name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22)))) selection = (chain 'C' and (resid 5 through 316 or resid 403 or (resid 404 and (name C1 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or name C3 \ 1 or name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C10 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 17 or name C18 or name C19)) or (resid 406 and (name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22)) or (resid 407 and (name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22)))) selection = (chain 'D' and (resid 5 through 316 or resid 403 or (resid 404 and (name C1 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or name C3 \ 1 or name C32 or name C33 or name O1P or name O2 or name O2P or name O3 or name \ O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 and (name C10 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 17 or name C18 or name C19)) or (resid 406 and (name C10 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22)) or (resid 407 and (name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22)))) selection = (chain 'E' and (resid 5 through 316 or (resid 403 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name O1P or name O2 or name O2P or name O3 or name O \ 3P or name O4 or name O4P or name O5 or name P )) or resid 404 or (resid 405 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 16 or name C17 or name C18 or name C19)) or (resid 406 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or (resid 407 and (name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C20 or name C21 or name C22)))) } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.850 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 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 : 0.004 0.030 13965 Z= 0.177 Angle : 0.822 5.715 18845 Z= 0.423 Chirality : 0.059 0.367 2100 Planarity : 0.011 0.067 2275 Dihedral : 19.327 154.281 5455 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1550 helix: 1.71 (0.20), residues: 520 sheet: 0.38 (0.26), residues: 420 loop : -1.02 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.005 ARG A 105 TYR 0.036 0.005 TYR D 263 PHE 0.038 0.004 PHE A 207 TRP 0.047 0.012 TRP B 217 HIS 0.004 0.002 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00379 (13965) covalent geometry : angle 0.82212 (18845) hydrogen bonds : bond 0.17346 ( 600) hydrogen bonds : angle 6.67388 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.504 Fit side-chains REVERT: A 64 LYS cc_start: 0.8613 (mttt) cc_final: 0.7884 (mtpp) REVERT: A 139 ASN cc_start: 0.8450 (m-40) cc_final: 0.8223 (m-40) REVERT: B 50 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7957 (ptp-110) REVERT: B 64 LYS cc_start: 0.8591 (mttt) cc_final: 0.7797 (mtpp) REVERT: B 139 ASN cc_start: 0.8514 (m-40) cc_final: 0.8294 (m-40) REVERT: B 180 LEU cc_start: 0.8585 (mt) cc_final: 0.8381 (mm) REVERT: C 50 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7868 (ptp-110) REVERT: C 88 ASP cc_start: 0.8294 (p0) cc_final: 0.7883 (p0) REVERT: C 139 ASN cc_start: 0.8443 (m-40) cc_final: 0.8175 (m-40) REVERT: D 55 ASP cc_start: 0.7666 (t0) cc_final: 0.6750 (p0) REVERT: D 64 LYS cc_start: 0.8519 (mttt) cc_final: 0.7857 (mtpm) REVERT: D 88 ASP cc_start: 0.8247 (p0) cc_final: 0.7704 (p0) REVERT: D 180 LEU cc_start: 0.8647 (mt) cc_final: 0.8338 (mm) REVERT: E 33 LYS cc_start: 0.9027 (mtmm) cc_final: 0.8767 (mttp) REVERT: E 55 ASP cc_start: 0.7552 (t0) cc_final: 0.6769 (p0) REVERT: E 91 ASP cc_start: 0.8256 (t70) cc_final: 0.8027 (t70) REVERT: E 200 ASN cc_start: 0.8518 (m-40) cc_final: 0.8300 (m-40) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.6209 time to fit residues: 146.5618 Evaluate side-chains 189 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN E 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.089234 restraints weight = 15636.544| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.84 r_work: 0.2731 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13965 Z= 0.127 Angle : 0.541 5.366 18845 Z= 0.279 Chirality : 0.043 0.149 2100 Planarity : 0.004 0.036 2275 Dihedral : 20.717 154.104 2530 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.14 % Allowed : 12.00 % Favored : 86.86 % 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: 1.20 (0.21), residues: 1550 helix: 2.85 (0.20), residues: 525 sheet: 0.32 (0.24), residues: 420 loop : -0.71 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 62 TYR 0.009 0.001 TYR E 102 PHE 0.008 0.001 PHE C 37 TRP 0.006 0.001 TRP E 160 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00285 (13965) covalent geometry : angle 0.54097 (18845) hydrogen bonds : bond 0.05696 ( 600) hydrogen bonds : angle 4.26517 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.547 Fit side-chains REVERT: B 180 LEU cc_start: 0.8687 (mt) cc_final: 0.8423 (mm) REVERT: B 181 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8496 (mt-10) REVERT: C 69 GLU cc_start: 0.7495 (mp0) cc_final: 0.7128 (mp0) REVERT: C 88 ASP cc_start: 0.8382 (p0) cc_final: 0.7869 (p0) REVERT: D 69 GLU cc_start: 0.7522 (mp0) cc_final: 0.7218 (mp0) REVERT: D 88 ASP cc_start: 0.8385 (p0) cc_final: 0.7826 (p0) REVERT: E 33 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8805 (mttp) REVERT: E 55 ASP cc_start: 0.7490 (t0) cc_final: 0.6623 (p0) REVERT: E 75 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: E 91 ASP cc_start: 0.8170 (t70) cc_final: 0.7820 (t70) REVERT: E 147 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 200 ASN cc_start: 0.8497 (m-40) cc_final: 0.8194 (m110) outliers start: 16 outliers final: 10 residues processed: 204 average time/residue: 0.5881 time to fit residues: 130.3061 Evaluate side-chains 210 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.088563 restraints weight = 15681.749| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.88 r_work: 0.2749 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13965 Z= 0.112 Angle : 0.506 5.986 18845 Z= 0.257 Chirality : 0.042 0.140 2100 Planarity : 0.004 0.034 2275 Dihedral : 19.937 153.059 2530 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.57 % Allowed : 12.64 % Favored : 86.79 % 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: 1.37 (0.21), residues: 1550 helix: 3.25 (0.21), residues: 525 sheet: 0.09 (0.23), residues: 455 loop : -0.64 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 62 TYR 0.011 0.001 TYR D 102 PHE 0.009 0.001 PHE D 37 TRP 0.004 0.001 TRP D 160 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00249 (13965) covalent geometry : angle 0.50607 (18845) hydrogen bonds : bond 0.05571 ( 600) hydrogen bonds : angle 3.87225 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 212 time to evaluate : 0.435 Fit side-chains REVERT: A 88 ASP cc_start: 0.8427 (p0) cc_final: 0.7796 (p0) REVERT: B 88 ASP cc_start: 0.8396 (p0) cc_final: 0.7805 (p0) REVERT: B 147 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 180 LEU cc_start: 0.8658 (mt) cc_final: 0.8410 (mm) REVERT: B 181 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8513 (mt-10) REVERT: C 69 GLU cc_start: 0.7545 (mp0) cc_final: 0.7211 (mp0) REVERT: C 181 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8477 (mt-10) REVERT: D 69 GLU cc_start: 0.7464 (mp0) cc_final: 0.7164 (mp0) REVERT: D 88 ASP cc_start: 0.8448 (p0) cc_final: 0.7840 (p0) REVERT: E 55 ASP cc_start: 0.7449 (t0) cc_final: 0.6581 (p0) REVERT: E 69 GLU cc_start: 0.7558 (mp0) cc_final: 0.7198 (mp0) REVERT: E 91 ASP cc_start: 0.8121 (t70) cc_final: 0.7685 (t70) REVERT: E 181 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8625 (mt-10) outliers start: 8 outliers final: 5 residues processed: 214 average time/residue: 0.5995 time to fit residues: 139.2548 Evaluate side-chains 204 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN B 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.083992 restraints weight = 15776.790| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.90 r_work: 0.2663 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13965 Z= 0.138 Angle : 0.536 6.167 18845 Z= 0.273 Chirality : 0.043 0.145 2100 Planarity : 0.004 0.034 2275 Dihedral : 19.664 156.965 2530 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.86 % Allowed : 11.86 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1550 helix: 3.26 (0.21), residues: 530 sheet: 0.12 (0.23), residues: 455 loop : -0.66 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 50 TYR 0.011 0.001 TYR C 102 PHE 0.009 0.001 PHE D 37 TRP 0.005 0.001 TRP C 160 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00324 (13965) covalent geometry : angle 0.53644 (18845) hydrogen bonds : bond 0.06581 ( 600) hydrogen bonds : angle 3.85665 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.320 Fit side-chains REVERT: A 88 ASP cc_start: 0.8467 (p0) cc_final: 0.7866 (p0) REVERT: A 181 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8777 (mt-10) REVERT: B 33 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8709 (mtmm) REVERT: B 88 ASP cc_start: 0.8467 (p0) cc_final: 0.7892 (p0) REVERT: B 147 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 181 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8588 (mt-10) REVERT: C 88 ASP cc_start: 0.8510 (p0) cc_final: 0.7914 (p0) REVERT: C 181 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8546 (mt-10) REVERT: D 69 GLU cc_start: 0.7505 (mp0) cc_final: 0.7192 (mp0) REVERT: D 75 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: D 181 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8743 (mt-10) REVERT: E 55 ASP cc_start: 0.7526 (t0) cc_final: 0.6588 (p0) REVERT: E 91 ASP cc_start: 0.8203 (t70) cc_final: 0.7761 (t70) REVERT: E 181 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8624 (mt-10) outliers start: 26 outliers final: 10 residues processed: 215 average time/residue: 0.5669 time to fit residues: 132.7093 Evaluate side-chains 210 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.079014 restraints weight = 15963.526| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.86 r_work: 0.2594 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13965 Z= 0.199 Angle : 0.595 6.629 18845 Z= 0.303 Chirality : 0.045 0.147 2100 Planarity : 0.005 0.031 2275 Dihedral : 19.993 164.348 2530 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 12.21 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1550 helix: 3.03 (0.21), residues: 530 sheet: -0.00 (0.23), residues: 420 loop : -0.72 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 50 TYR 0.010 0.002 TYR D 102 PHE 0.009 0.001 PHE C 37 TRP 0.005 0.001 TRP D 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00495 (13965) covalent geometry : angle 0.59477 (18845) hydrogen bonds : bond 0.08128 ( 600) hydrogen bonds : angle 4.10774 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.538 Fit side-chains REVERT: A 88 ASP cc_start: 0.8466 (p0) cc_final: 0.7906 (p0) REVERT: A 181 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8819 (mt-10) REVERT: A 280 LYS cc_start: 0.8018 (tttm) cc_final: 0.7589 (ttmm) REVERT: B 33 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8738 (mtmm) REVERT: B 75 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8456 (mt-10) REVERT: B 147 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 181 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8600 (mt-10) REVERT: C 88 ASP cc_start: 0.8533 (p0) cc_final: 0.7917 (p0) REVERT: C 181 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8641 (mt-10) REVERT: D 69 GLU cc_start: 0.7529 (mp0) cc_final: 0.7212 (mp0) REVERT: D 181 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8796 (mt-10) REVERT: E 55 ASP cc_start: 0.7553 (t0) cc_final: 0.6565 (p0) REVERT: E 91 ASP cc_start: 0.8219 (t70) cc_final: 0.7771 (t70) REVERT: E 181 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8671 (mt-10) REVERT: E 280 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7646 (ttmm) outliers start: 29 outliers final: 13 residues processed: 214 average time/residue: 0.5896 time to fit residues: 137.2469 Evaluate side-chains 206 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.084170 restraints weight = 15746.100| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.85 r_work: 0.2656 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13965 Z= 0.109 Angle : 0.504 6.525 18845 Z= 0.257 Chirality : 0.042 0.135 2100 Planarity : 0.004 0.035 2275 Dihedral : 19.048 164.111 2530 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.43 % Allowed : 12.79 % Favored : 85.79 % 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: 1.51 (0.21), residues: 1550 helix: 3.38 (0.21), residues: 530 sheet: 0.11 (0.23), residues: 455 loop : -0.56 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 50 TYR 0.013 0.001 TYR D 102 PHE 0.006 0.001 PHE C 37 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00235 (13965) covalent geometry : angle 0.50428 (18845) hydrogen bonds : bond 0.05604 ( 600) hydrogen bonds : angle 3.72926 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.450 Fit side-chains REVERT: A 88 ASP cc_start: 0.8383 (p0) cc_final: 0.7828 (p0) REVERT: B 75 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: B 88 ASP cc_start: 0.8403 (p0) cc_final: 0.7866 (p0) REVERT: B 147 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 181 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 88 ASP cc_start: 0.8458 (p0) cc_final: 0.7845 (p0) REVERT: C 181 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8569 (mt-10) REVERT: D 75 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8432 (mt-10) REVERT: D 181 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8767 (mt-10) REVERT: E 55 ASP cc_start: 0.7538 (t0) cc_final: 0.6526 (p0) REVERT: E 69 GLU cc_start: 0.7539 (mp0) cc_final: 0.7256 (mp0) REVERT: E 147 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 181 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8620 (mt-10) outliers start: 20 outliers final: 11 residues processed: 209 average time/residue: 0.6416 time to fit residues: 145.8181 Evaluate side-chains 207 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.079583 restraints weight = 15885.361| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.85 r_work: 0.2565 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13965 Z= 0.217 Angle : 0.599 6.501 18845 Z= 0.305 Chirality : 0.045 0.143 2100 Planarity : 0.005 0.033 2275 Dihedral : 19.474 168.843 2530 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.71 % Allowed : 13.21 % Favored : 85.07 % 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: 1.13 (0.21), residues: 1550 helix: 3.03 (0.21), residues: 530 sheet: -0.04 (0.23), residues: 415 loop : -0.76 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 50 TYR 0.010 0.002 TYR D 102 PHE 0.009 0.002 PHE A 195 TRP 0.005 0.001 TRP D 160 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00544 (13965) covalent geometry : angle 0.59909 (18845) hydrogen bonds : bond 0.08171 ( 600) hydrogen bonds : angle 4.05562 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.537 Fit side-chains REVERT: A 88 ASP cc_start: 0.8440 (p0) cc_final: 0.7878 (p0) REVERT: A 181 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8886 (mm-30) REVERT: A 280 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7536 (ttmm) REVERT: B 88 ASP cc_start: 0.8458 (p0) cc_final: 0.7859 (p0) REVERT: B 147 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 181 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8644 (mt-10) REVERT: C 88 ASP cc_start: 0.8524 (p0) cc_final: 0.7901 (p0) REVERT: C 181 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8690 (mt-10) REVERT: D 88 ASP cc_start: 0.8552 (p0) cc_final: 0.7902 (p0) REVERT: D 181 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8753 (mt-10) REVERT: E 55 ASP cc_start: 0.7584 (t0) cc_final: 0.6587 (p0) REVERT: E 147 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8318 (mm-30) REVERT: E 181 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8716 (mt-10) REVERT: E 280 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7613 (ttmm) outliers start: 24 outliers final: 15 residues processed: 194 average time/residue: 0.6756 time to fit residues: 141.9576 Evaluate side-chains 197 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.083431 restraints weight = 15695.842| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.89 r_work: 0.2656 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13965 Z= 0.127 Angle : 0.522 6.637 18845 Z= 0.266 Chirality : 0.043 0.138 2100 Planarity : 0.004 0.037 2275 Dihedral : 18.694 167.164 2530 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.29 % Allowed : 13.86 % Favored : 84.86 % 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: 1.40 (0.21), residues: 1550 helix: 3.28 (0.21), residues: 530 sheet: 0.05 (0.23), residues: 455 loop : -0.61 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 50 TYR 0.013 0.001 TYR D 102 PHE 0.006 0.001 PHE C 37 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00292 (13965) covalent geometry : angle 0.52201 (18845) hydrogen bonds : bond 0.06254 ( 600) hydrogen bonds : angle 3.82128 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.508 Fit side-chains REVERT: A 88 ASP cc_start: 0.8387 (p0) cc_final: 0.7846 (p0) REVERT: A 181 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8896 (mm-30) REVERT: A 280 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7326 (ttmm) REVERT: B 88 ASP cc_start: 0.8435 (p0) cc_final: 0.7860 (p0) REVERT: B 147 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 181 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8600 (mt-10) REVERT: C 88 ASP cc_start: 0.8447 (p0) cc_final: 0.7869 (p0) REVERT: C 181 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8633 (mt-10) REVERT: D 181 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 55 ASP cc_start: 0.7539 (t0) cc_final: 0.6528 (p0) REVERT: E 139 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8161 (t0) REVERT: E 147 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8305 (mm-30) REVERT: E 181 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8637 (mt-10) REVERT: E 280 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7420 (ttmm) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 0.6662 time to fit residues: 144.9624 Evaluate side-chains 204 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.084037 restraints weight = 15736.214| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.89 r_work: 0.2666 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13965 Z= 0.121 Angle : 0.514 6.203 18845 Z= 0.263 Chirality : 0.043 0.136 2100 Planarity : 0.004 0.043 2275 Dihedral : 18.099 162.510 2530 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.29 % Allowed : 14.07 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1550 helix: 3.33 (0.21), residues: 530 sheet: 0.07 (0.23), residues: 455 loop : -0.60 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 50 TYR 0.012 0.001 TYR D 102 PHE 0.006 0.001 PHE B 37 TRP 0.005 0.001 TRP D 160 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00275 (13965) covalent geometry : angle 0.51434 (18845) hydrogen bonds : bond 0.06035 ( 600) hydrogen bonds : angle 3.74030 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.539 Fit side-chains REVERT: A 88 ASP cc_start: 0.8371 (p0) cc_final: 0.7826 (p0) REVERT: A 181 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8862 (mm-30) REVERT: A 280 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7247 (ttmm) REVERT: B 88 ASP cc_start: 0.8415 (p0) cc_final: 0.7843 (p0) REVERT: B 101 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: B 147 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 181 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8597 (mt-10) REVERT: C 88 ASP cc_start: 0.8427 (p0) cc_final: 0.7838 (p0) REVERT: C 181 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8645 (mt-10) REVERT: D 181 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8800 (mt-10) REVERT: E 55 ASP cc_start: 0.7552 (t0) cc_final: 0.6534 (p0) REVERT: E 139 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8165 (t0) REVERT: E 147 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8313 (mm-30) REVERT: E 181 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8642 (mt-10) outliers start: 18 outliers final: 13 residues processed: 194 average time/residue: 0.6976 time to fit residues: 146.6633 Evaluate side-chains 204 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.083641 restraints weight = 15637.797| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.89 r_work: 0.2625 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13965 Z= 0.130 Angle : 0.520 6.224 18845 Z= 0.265 Chirality : 0.043 0.136 2100 Planarity : 0.004 0.041 2275 Dihedral : 17.842 157.870 2530 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.07 % Allowed : 14.07 % Favored : 84.86 % 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: 1.43 (0.21), residues: 1550 helix: 3.30 (0.21), residues: 530 sheet: 0.07 (0.23), residues: 455 loop : -0.61 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 50 TYR 0.012 0.001 TYR D 102 PHE 0.006 0.001 PHE B 37 TRP 0.004 0.001 TRP C 160 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00305 (13965) covalent geometry : angle 0.51957 (18845) hydrogen bonds : bond 0.06206 ( 600) hydrogen bonds : angle 3.74650 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.536 Fit side-chains REVERT: A 88 ASP cc_start: 0.8377 (p0) cc_final: 0.7838 (p0) REVERT: A 181 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8866 (mm-30) REVERT: A 280 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7293 (ttmm) REVERT: B 88 ASP cc_start: 0.8420 (p0) cc_final: 0.7855 (p0) REVERT: B 147 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8269 (mm-30) REVERT: B 181 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8607 (mt-10) REVERT: C 88 ASP cc_start: 0.8436 (p0) cc_final: 0.7854 (p0) REVERT: C 181 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8669 (mt-10) REVERT: D 181 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8801 (mt-10) REVERT: E 55 ASP cc_start: 0.7548 (t0) cc_final: 0.6537 (p0) REVERT: E 139 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: E 147 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8327 (mm-30) REVERT: E 181 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8672 (mt-10) outliers start: 15 outliers final: 13 residues processed: 194 average time/residue: 0.6403 time to fit residues: 134.5115 Evaluate side-chains 200 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 31 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.085782 restraints weight = 15708.238| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.89 r_work: 0.2651 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13965 Z= 0.104 Angle : 0.496 6.108 18845 Z= 0.254 Chirality : 0.042 0.133 2100 Planarity : 0.004 0.046 2275 Dihedral : 17.164 147.846 2530 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.00 % Allowed : 14.29 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1550 helix: 3.45 (0.21), residues: 530 sheet: 0.12 (0.23), residues: 455 loop : -0.55 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 50 TYR 0.013 0.001 TYR D 102 PHE 0.005 0.001 PHE B 37 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00219 (13965) covalent geometry : angle 0.49644 (18845) hydrogen bonds : bond 0.05370 ( 600) hydrogen bonds : angle 3.63076 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.18 seconds wall clock time: 68 minutes 40.86 seconds (4120.86 seconds total)