Starting phenix.real_space_refine on Fri Jul 3 12:21:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lba_62938/07_2026/9lba_62938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lba_62938/07_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_62938/07_2026/9lba_62938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lba_62938/07_2026/9lba_62938.map" model { file = "/net/cci-nas-00/data/ceres_data/9lba_62938/07_2026/9lba_62938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lba_62938/07_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-dev-6108/lib/python3.11/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, 230 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 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, 203 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 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, 203 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 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, 203 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 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, 176 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 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: 2.37, per 1000 atoms: 0.17 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: 1.14 Conformation dependent library (CDL) restraints added in 548.3 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: 0.24 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: 1.97 Time building geometry restraints manager: 1.52 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: 1.600 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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/Z covalent geometry : bond 0.00379 / 0.18 (13965) covalent geometry : angle 0.82212 / 0.42 (18845) hydrogen bonds : bond 0.17346 / 11.41 ( 600) hydrogen bonds : angle 6.67388 / 4.60 ( 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 : 0.364 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: 0.5123 time to fit residues: 121.6388 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 : 0.334 ------------------------------------------------------------------------------- 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... 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 = 0.3260 r_free = 0.3260 target = 0.115556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.089654 restraints weight = 15642.463| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.83 r_work: 0.2713 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0968 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= 0.124 Angle : 0.537 5.309 18845 Z= 0.277 Chirality : 0.043 0.147 2100 Planarity : 0.004 0.036 2275 Dihedral : 20.771 154.126 2530 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 12.14 % 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: 1.21 (0.21), residues: 1550 helix: 2.85 (0.20), residues: 525 sheet: 0.34 (0.24), residues: 420 loop : -0.71 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 50 TYR 0.010 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/Z covalent geometry : bond 0.00281 / 0.12 (13965) covalent geometry : angle 0.53713 / 0.28 (18845) hydrogen bonds : bond 0.05709 / 3.77 ( 600) hydrogen bonds : angle 4.29877 / 2.92 ( 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 214 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.493 Fit side-chains REVERT: A 101 GLN cc_start: 0.8894 (tp40) cc_final: 0.8659 (tp40) REVERT: B 180 LEU cc_start: 0.8685 (mt) cc_final: 0.8424 (mm) REVERT: B 181 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 69 GLU cc_start: 0.7490 (mp0) cc_final: 0.7122 (mp0) REVERT: C 88 ASP cc_start: 0.8385 (p0) cc_final: 0.7874 (p0) REVERT: D 69 GLU cc_start: 0.7520 (mp0) cc_final: 0.7210 (mp0) REVERT: D 88 ASP cc_start: 0.8374 (p0) cc_final: 0.7823 (p0) REVERT: E 33 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8805 (mttp) REVERT: E 55 ASP cc_start: 0.7494 (t0) cc_final: 0.6623 (p0) REVERT: E 91 ASP cc_start: 0.8172 (t70) cc_final: 0.7821 (t70) REVERT: E 147 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 200 ASN cc_start: 0.8497 (m-40) cc_final: 0.8200 (m110) outliers start: 14 outliers final: 10 residues processed: 205 average time/residue: 0.5319 time to fit residues: 118.6073 Evaluate side-chains 208 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.081597 restraints weight = 15899.458| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.90 r_work: 0.2603 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1673 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= 0.185 Angle : 0.591 6.539 18845 Z= 0.300 Chirality : 0.045 0.142 2100 Planarity : 0.004 0.034 2275 Dihedral : 20.620 157.941 2530 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 11.71 % 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: 1.15 (0.21), residues: 1550 helix: 3.01 (0.21), residues: 525 sheet: 0.11 (0.23), residues: 420 loop : -0.81 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 50 TYR 0.012 0.002 TYR D 102 PHE 0.011 0.002 PHE D 37 TRP 0.006 0.001 TRP C 160 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (13965) covalent geometry : angle 0.59120 / 0.30 (18845) hydrogen bonds : bond 0.07879 / 5.23 ( 600) hydrogen bonds : angle 4.17929 / 2.84 ( 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 211 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.322 Fit side-chains REVERT: A 88 ASP cc_start: 0.8507 (p0) cc_final: 0.7893 (p0) REVERT: B 88 ASP cc_start: 0.8478 (p0) cc_final: 0.7867 (p0) REVERT: B 181 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8602 (mt-10) REVERT: C 88 ASP cc_start: 0.8523 (p0) cc_final: 0.7922 (p0) REVERT: C 181 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8578 (mt-10) REVERT: D 69 GLU cc_start: 0.7555 (mp0) cc_final: 0.7254 (mp0) REVERT: D 75 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: D 88 ASP cc_start: 0.8534 (p0) cc_final: 0.7926 (p0) REVERT: E 55 ASP cc_start: 0.7512 (t0) cc_final: 0.6555 (p0) REVERT: E 91 ASP cc_start: 0.8244 (t70) cc_final: 0.7810 (t70) REVERT: E 147 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8322 (mm-30) REVERT: E 181 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8642 (mt-10) REVERT: E 280 LYS cc_start: 0.8092 (tttt) cc_final: 0.7638 (ttmm) outliers start: 21 outliers final: 12 residues processed: 200 average time/residue: 0.5778 time to fit residues: 125.9622 Evaluate side-chains 197 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 63 VAL 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 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: 2.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.079206 restraints weight = 15922.383| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.91 r_work: 0.2558 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13965 Z= 0.213 Angle : 0.613 7.155 18845 Z= 0.312 Chirality : 0.045 0.144 2100 Planarity : 0.005 0.034 2275 Dihedral : 20.904 170.051 2530 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.50 % Allowed : 11.36 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1550 helix: 2.90 (0.20), residues: 530 sheet: -0.10 (0.24), residues: 380 loop : -1.01 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 50 TYR 0.011 0.002 TYR E 102 PHE 0.010 0.002 PHE C 37 TRP 0.007 0.001 TRP C 160 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.21 (13965) covalent geometry : angle 0.61350 / 0.31 (18845) hydrogen bonds : bond 0.08440 / 5.61 ( 600) hydrogen bonds : angle 4.24981 / 2.89 ( 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 213 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.538 Fit side-chains REVERT: A 88 ASP cc_start: 0.8486 (p0) cc_final: 0.7897 (p0) REVERT: A 280 LYS cc_start: 0.8070 (tttm) cc_final: 0.7650 (ttmm) REVERT: B 88 ASP cc_start: 0.8433 (p0) cc_final: 0.7855 (p0) REVERT: B 181 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8641 (mt-10) REVERT: C 88 ASP cc_start: 0.8524 (p0) cc_final: 0.7920 (p0) REVERT: C 181 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 69 GLU cc_start: 0.7525 (mp0) cc_final: 0.7240 (mp0) REVERT: D 181 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8754 (mt-10) REVERT: E 55 ASP cc_start: 0.7572 (t0) cc_final: 0.6580 (p0) REVERT: E 91 ASP cc_start: 0.8260 (t70) cc_final: 0.7820 (t70) REVERT: E 147 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 181 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8700 (mt-10) REVERT: E 280 LYS cc_start: 0.8154 (tttt) cc_final: 0.7707 (ttmm) outliers start: 35 outliers final: 16 residues processed: 194 average time/residue: 0.5765 time to fit residues: 121.3112 Evaluate side-chains 187 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 63 VAL 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 63 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.080181 restraints weight = 15914.440| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.91 r_work: 0.2586 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13965 Z= 0.176 Angle : 0.571 6.974 18845 Z= 0.291 Chirality : 0.044 0.141 2100 Planarity : 0.004 0.034 2275 Dihedral : 20.639 178.426 2530 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.86 % Allowed : 12.00 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1550 helix: 3.01 (0.20), residues: 530 sheet: -0.07 (0.24), residues: 380 loop : -1.00 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.012 0.001 TYR D 102 PHE 0.007 0.001 PHE C 37 TRP 0.006 0.001 TRP E 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13965) covalent geometry : angle 0.57052 / 0.29 (18845) hydrogen bonds : bond 0.07654 / 5.10 ( 600) hydrogen bonds : angle 4.10166 / 2.79 ( 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 206 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.406 Fit side-chains REVERT: A 88 ASP cc_start: 0.8433 (p0) cc_final: 0.7857 (p0) REVERT: A 181 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8907 (mm-30) REVERT: A 280 LYS cc_start: 0.7912 (tttm) cc_final: 0.7495 (ttmm) REVERT: B 88 ASP cc_start: 0.8412 (p0) cc_final: 0.7818 (p0) REVERT: B 147 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 181 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8639 (mt-10) REVERT: C 88 ASP cc_start: 0.8511 (p0) cc_final: 0.7932 (p0) REVERT: C 181 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8694 (mt-10) REVERT: D 88 ASP cc_start: 0.8515 (p0) cc_final: 0.7868 (p0) REVERT: D 181 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8734 (mt-10) REVERT: E 55 ASP cc_start: 0.7557 (t0) cc_final: 0.6548 (p0) REVERT: E 75 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: E 147 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 181 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8699 (mt-10) REVERT: E 280 LYS cc_start: 0.8055 (tttt) cc_final: 0.7599 (ttmm) outliers start: 26 outliers final: 17 residues processed: 188 average time/residue: 0.5775 time to fit residues: 117.6998 Evaluate side-chains 208 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 48 LYS 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 63 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU 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 75 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 27 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084967 restraints weight = 15743.923| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.85 r_work: 0.2694 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13965 Z= 0.105 Angle : 0.498 6.520 18845 Z= 0.254 Chirality : 0.042 0.129 2100 Planarity : 0.004 0.036 2275 Dihedral : 19.611 175.149 2530 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.36 % Allowed : 12.43 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1550 helix: 3.37 (0.21), residues: 530 sheet: 0.08 (0.23), residues: 455 loop : -0.61 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 50 TYR 0.014 0.001 TYR D 102 PHE 0.006 0.001 PHE D 37 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (13965) covalent geometry : angle 0.49830 / 0.25 (18845) hydrogen bonds : bond 0.05395 / 3.61 ( 600) hydrogen bonds : angle 3.71023 / 2.52 ( 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 218 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.380 Fit side-chains REVERT: A 88 ASP cc_start: 0.8352 (p0) cc_final: 0.7809 (p0) REVERT: B 88 ASP cc_start: 0.8356 (p0) cc_final: 0.7811 (p0) REVERT: B 101 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: B 147 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 181 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8584 (mt-10) REVERT: C 88 ASP cc_start: 0.8441 (p0) cc_final: 0.7863 (p0) REVERT: C 181 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8624 (mt-10) REVERT: D 181 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8794 (mt-10) REVERT: E 55 ASP cc_start: 0.7534 (t0) cc_final: 0.6513 (p0) REVERT: E 147 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 181 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8634 (mt-10) outliers start: 19 outliers final: 4 residues processed: 202 average time/residue: 0.5519 time to fit residues: 121.0038 Evaluate side-chains 199 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU 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: 4.9990 chunk 107 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 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: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 307 ASN E 101 GLN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.078942 restraints weight = 15885.204| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.85 r_work: 0.2569 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2112 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= 0.197 Angle : 0.582 6.382 18845 Z= 0.297 Chirality : 0.045 0.142 2100 Planarity : 0.004 0.033 2275 Dihedral : 19.846 173.150 2530 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.64 % Allowed : 13.43 % Favored : 84.93 % 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: 1.02 (0.21), residues: 1550 helix: 3.07 (0.21), residues: 530 sheet: -0.04 (0.24), residues: 380 loop : -0.96 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 50 TYR 0.011 0.002 TYR D 102 PHE 0.008 0.001 PHE B 116 TRP 0.005 0.001 TRP A 160 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (13965) covalent geometry : angle 0.58172 / 0.30 (18845) hydrogen bonds : bond 0.07882 / 5.24 ( 600) hydrogen bonds : angle 4.02610 / 2.74 ( 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 203 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.418 Fit side-chains REVERT: A 88 ASP cc_start: 0.8446 (p0) cc_final: 0.7920 (p0) REVERT: A 280 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7522 (ttmm) REVERT: B 88 ASP cc_start: 0.8416 (p0) cc_final: 0.7858 (p0) REVERT: B 147 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8630 (mt-10) REVERT: C 88 ASP cc_start: 0.8507 (p0) cc_final: 0.7931 (p0) REVERT: C 181 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8737 (mt-10) REVERT: D 181 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8782 (mt-10) REVERT: E 55 ASP cc_start: 0.7591 (t0) cc_final: 0.6583 (p0) REVERT: E 139 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (t0) REVERT: E 147 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8283 (mm-30) REVERT: E 181 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 280 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7562 (ttmm) outliers start: 23 outliers final: 12 residues processed: 189 average time/residue: 0.5747 time to fit residues: 118.0768 Evaluate side-chains 194 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.085224 restraints weight = 15585.466| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.88 r_work: 0.2694 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13965 Z= 0.105 Angle : 0.503 6.355 18845 Z= 0.258 Chirality : 0.043 0.134 2100 Planarity : 0.004 0.035 2275 Dihedral : 19.079 167.919 2530 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.07 % Allowed : 14.00 % Favored : 84.93 % 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: 1.50 (0.21), residues: 1550 helix: 3.40 (0.21), residues: 530 sheet: 0.08 (0.23), residues: 455 loop : -0.58 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 50 TYR 0.014 0.001 TYR D 102 PHE 0.005 0.001 PHE E 42 TRP 0.005 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (13965) covalent geometry : angle 0.50325 / 0.26 (18845) hydrogen bonds : bond 0.05575 / 3.73 ( 600) hydrogen bonds : angle 3.72901 / 2.54 ( 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 205 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.539 Fit side-chains REVERT: A 88 ASP cc_start: 0.8366 (p0) cc_final: 0.7829 (p0) REVERT: A 280 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7227 (ttmm) REVERT: A 307 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8715 (m-40) REVERT: B 88 ASP cc_start: 0.8346 (p0) cc_final: 0.7796 (p0) REVERT: B 101 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: B 147 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 181 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8588 (mt-10) REVERT: C 181 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8659 (mt-10) REVERT: D 62 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: D 181 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8623 (mt-10) REVERT: E 55 ASP cc_start: 0.7548 (t0) cc_final: 0.6525 (p0) REVERT: E 139 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: E 147 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8268 (mm-30) REVERT: E 181 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8670 (mt-10) outliers start: 15 outliers final: 7 residues processed: 192 average time/residue: 0.5610 time to fit residues: 116.9759 Evaluate side-chains 199 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 180 LEU 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: 0.0570 chunk 27 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084682 restraints weight = 15644.208| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.89 r_work: 0.2637 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2037 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= 0.118 Angle : 0.507 6.073 18845 Z= 0.259 Chirality : 0.043 0.133 2100 Planarity : 0.004 0.048 2275 Dihedral : 18.804 162.118 2530 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 14.43 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1550 helix: 3.38 (0.21), residues: 530 sheet: 0.08 (0.23), residues: 455 loop : -0.57 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 50 TYR 0.013 0.001 TYR D 102 PHE 0.006 0.001 PHE C 37 TRP 0.004 0.001 TRP B 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13965) covalent geometry : angle 0.50721 / 0.26 (18845) hydrogen bonds : bond 0.05848 / 3.91 ( 600) hydrogen bonds : angle 3.69665 / 2.51 ( 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 204 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.342 Fit side-chains REVERT: A 88 ASP cc_start: 0.8361 (p0) cc_final: 0.7812 (p0) REVERT: A 147 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8291 (mm-30) REVERT: A 280 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7228 (ttmm) REVERT: A 307 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8721 (m-40) REVERT: B 88 ASP cc_start: 0.8348 (p0) cc_final: 0.7787 (p0) REVERT: B 101 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: B 147 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8321 (mm-30) REVERT: B 181 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 88 ASP cc_start: 0.8453 (p0) cc_final: 0.7852 (p0) REVERT: C 181 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8678 (mt-10) REVERT: D 62 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: D 181 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8644 (mt-10) REVERT: E 55 ASP cc_start: 0.7569 (t0) cc_final: 0.6549 (p0) REVERT: E 139 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8225 (t0) REVERT: E 147 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 181 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8679 (mt-10) outliers start: 16 outliers final: 9 residues processed: 194 average time/residue: 0.5551 time to fit residues: 116.9148 Evaluate side-chains 201 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 ASN 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 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: 0.9980 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.085369 restraints weight = 15534.326| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.88 r_work: 0.2681 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13965 Z= 0.111 Angle : 0.500 6.130 18845 Z= 0.255 Chirality : 0.043 0.133 2100 Planarity : 0.004 0.035 2275 Dihedral : 18.404 160.642 2530 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 14.86 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1550 helix: 3.41 (0.21), residues: 530 sheet: 0.10 (0.23), residues: 455 loop : -0.55 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 50 TYR 0.013 0.001 TYR D 102 PHE 0.005 0.001 PHE C 37 TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13965) covalent geometry : angle 0.49981 / 0.26 (18845) hydrogen bonds : bond 0.05630 / 3.76 ( 600) hydrogen bonds : angle 3.65573 / 2.49 ( 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 208 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.381 Fit side-chains REVERT: A 88 ASP cc_start: 0.8354 (p0) cc_final: 0.7809 (p0) REVERT: A 147 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 280 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7189 (ttmm) REVERT: B 88 ASP cc_start: 0.8342 (p0) cc_final: 0.7794 (p0) REVERT: B 101 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: B 147 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 181 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8608 (mt-10) REVERT: C 181 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8658 (mt-10) REVERT: D 62 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7605 (mmm-85) REVERT: D 181 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8635 (mt-10) REVERT: E 55 ASP cc_start: 0.7555 (t0) cc_final: 0.6533 (p0) REVERT: E 139 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (t0) REVERT: E 147 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8278 (mm-30) REVERT: E 181 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8666 (mt-10) outliers start: 14 outliers final: 9 residues processed: 197 average time/residue: 0.5483 time to fit residues: 117.5009 Evaluate side-chains 200 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 7.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN C 307 ASN E 101 GLN E 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.079253 restraints weight = 15805.539| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.84 r_work: 0.2582 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13965 Z= 0.218 Angle : 0.606 6.691 18845 Z= 0.309 Chirality : 0.045 0.141 2100 Planarity : 0.005 0.039 2275 Dihedral : 18.888 158.166 2530 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.29 % Allowed : 14.29 % Favored : 84.43 % 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: 0.96 (0.21), residues: 1550 helix: 3.00 (0.21), residues: 530 sheet: -0.07 (0.24), residues: 380 loop : -0.98 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 50 TYR 0.010 0.002 TYR D 102 PHE 0.010 0.002 PHE E 195 TRP 0.006 0.001 TRP D 213 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (13965) covalent geometry : angle 0.60608 / 0.31 (18845) hydrogen bonds : bond 0.08280 / 5.51 ( 600) hydrogen bonds : angle 4.05446 / 2.76 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.22 seconds wall clock time: 62 minutes 47.63 seconds (3767.63 seconds total)