Starting phenix.real_space_refine on Wed Feb 4 21:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbb_62939/02_2026/9lbb_62939.map" } resolution = 3.45 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 20 5.16 5 C 8586 2.51 5 N 2034 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13002 Number of models: 1 Model: "" Number of chains: 10 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: "D" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 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: "B" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 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: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 58 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 65 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 43 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 14 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG D 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.47 residue: pdb=" N AARG B 293 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 293 " occ=0.50 Time building chain proxies: 3.95, per 1000 atoms: 0.30 Number of scatterers: 13002 At special positions: 0 Unit cell: (102.6, 93.48, 129.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 10 15.00 O 2352 8.00 N 2034 7.00 C 8586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 694.3 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3054 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 18 sheets defined 38.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.069A pdb=" N ILE A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 214 removed outlier: 5.044A 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 215 through 218 removed outlier: 3.515A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.913A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.514A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 5.150A 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: 3.677A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 245 removed outlier: 4.067A pdb=" N ASN D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.565A pdb=" N GLU D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.545A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.776A 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 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 197 through 214 removed outlier: 5.561A 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 215 through 218 removed outlier: 3.779A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.558A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.625A pdb=" N ALA B 53 " --> pdb=" O ARG B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 5.195A 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 215 through 218 removed outlier: 3.572A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 246 removed outlier: 4.156A pdb=" N ASN B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.572A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 297 " --> pdb=" O AARG 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: 3.989A 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 214 removed outlier: 3.635A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.715A 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 215 through 218 removed outlier: 3.664A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.635A pdb=" N ALA C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.537A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 31 removed outlier: 5.320A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 92 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.597A pdb=" N LEU A 126 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 16 through 20 Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 94 removed outlier: 4.015A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 43 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 108 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.609A pdb=" N ILE D 190 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 88 through 91 removed outlier: 5.717A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN E 19 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 88 through 91 removed outlier: 5.717A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN E 19 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 150 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.577A pdb=" N VAL E 132 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.577A pdb=" N VAL E 132 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 16 through 17 removed outlier: 6.484A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.826A pdb=" N ASP B 86 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 107 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.826A pdb=" N ASP B 86 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 107 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 43 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 108 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.672A pdb=" N ILE B 190 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.234A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.730A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 64 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.199A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.564A pdb=" N VAL C 132 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER C 182 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1754 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: 1.86 Time building geometry restraints manager: 1.31 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: 2147 1.32 - 1.45: 3587 1.45 - 1.57: 7545 1.57 - 1.69: 20 1.69 - 1.81: 35 Bond restraints: 13334 Sorted by residual: bond pdb=" N PHE A 116 " pdb=" CA PHE A 116 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.32e-02 5.74e+03 5.83e+00 bond pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.33e-02 5.65e+03 4.27e+00 bond pdb=" N PHE D 116 " pdb=" CA PHE D 116 " ideal model delta sigma weight residual 1.464 1.482 -0.019 1.20e-02 6.94e+03 2.38e+00 bond pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.30e-02 1.89e+03 1.39e+00 bond pdb=" CB LYS A 33 " pdb=" CG LYS A 33 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 ... (remaining 13329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17937 2.09 - 4.18: 182 4.18 - 6.27: 33 6.27 - 8.37: 6 8.37 - 10.46: 1 Bond angle restraints: 18159 Sorted by residual: angle pdb=" C LYS B 64 " pdb=" N THR B 65 " pdb=" CA THR B 65 " ideal model delta sigma weight residual 122.40 130.14 -7.74 1.45e+00 4.76e-01 2.85e+01 angle pdb=" C ALA D 175 " pdb=" CA ALA D 175 " pdb=" CB ALA D 175 " ideal model delta sigma weight residual 115.89 110.53 5.36 1.32e+00 5.74e-01 1.65e+01 angle pdb=" CA LYS B 170 " pdb=" CB LYS B 170 " pdb=" CG LYS B 170 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CB LYS A 33 " pdb=" CG LYS A 33 " pdb=" CD LYS A 33 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 angle pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 ... (remaining 18154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 7671 33.21 - 66.41: 273 66.41 - 99.62: 26 99.62 - 132.83: 5 132.83 - 166.04: 5 Dihedral angle restraints: 7980 sinusoidal: 3292 harmonic: 4688 Sorted by residual: dihedral pdb=" C3 PEE E 402 " pdb=" C1 PEE E 402 " pdb=" C2 PEE E 402 " pdb=" O3P PEE E 402 " ideal model delta sinusoidal sigma weight residual 62.73 -131.23 -166.04 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O2 PEE E 402 " pdb=" C1 PEE E 402 " pdb=" C2 PEE E 402 " pdb=" O3P PEE E 402 " ideal model delta sinusoidal sigma weight residual -59.96 104.30 -164.26 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O2 PEE C 401 " pdb=" C1 PEE C 401 " pdb=" C2 PEE C 401 " pdb=" O3P PEE C 401 " ideal model delta sinusoidal sigma weight residual 300.04 145.52 154.52 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 7977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1496 0.041 - 0.082: 408 0.082 - 0.122: 166 0.122 - 0.163: 14 0.163 - 0.204: 3 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA ASP A 55 " pdb=" N ASP A 55 " pdb=" C ASP A 55 " pdb=" CB ASP A 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA THR B 65 " pdb=" N THR B 65 " pdb=" C THR B 65 " pdb=" CB THR B 65 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA VAL E 61 " pdb=" N VAL E 61 " pdb=" C VAL E 61 " pdb=" CB VAL E 61 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 2084 not shown) Planarity restraints: 2251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 95 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO E 96 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 102 " -0.004 2.00e-02 2.50e+03 1.09e-02 2.37e+00 pdb=" CG TYR D 102 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 102 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 102 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR D 102 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 102 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 102 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 102 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 64 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C LYS B 64 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS B 64 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 65 " 0.008 2.00e-02 2.50e+03 ... (remaining 2248 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2049 2.76 - 3.30: 11972 3.30 - 3.83: 20500 3.83 - 4.37: 22493 4.37 - 4.90: 41466 Nonbonded interactions: 98480 Sorted by model distance: nonbonded pdb=" OE1 GLU A 82 " pdb=" OH TYR E 28 " model vdw 2.229 3.040 nonbonded pdb=" O GLY A 60 " pdb=" NZ LYS A 64 " model vdw 2.285 3.120 nonbonded pdb=" OE1 GLN A 284 " pdb=" NH1 ARG A 287 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS C 48 " pdb=" O ASP C 97 " model vdw 2.314 3.120 nonbonded pdb=" O SER D 6 " pdb=" NH2 ARG D 51 " model vdw 2.327 3.120 ... (remaining 98475 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 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.003 0.032 13334 Z= 0.130 Angle : 0.563 10.458 18159 Z= 0.296 Chirality : 0.043 0.204 2087 Planarity : 0.004 0.041 2251 Dihedral : 17.132 166.036 4926 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 21.11 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1556 helix: 3.56 (0.21), residues: 495 sheet: -0.64 (0.27), residues: 371 loop : -1.74 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.023 0.001 TYR D 102 PHE 0.021 0.001 PHE D 106 TRP 0.009 0.001 TRP E 72 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00279 (13334) covalent geometry : angle 0.56346 (18159) hydrogen bonds : bond 0.16508 ( 571) hydrogen bonds : angle 6.48598 ( 1754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 154 ASP cc_start: 0.7844 (m-30) cc_final: 0.6975 (t0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1029 time to fit residues: 30.2713 Evaluate side-chains 178 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113629 restraints weight = 17518.338| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.51 r_work: 0.2985 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13334 Z= 0.151 Angle : 0.574 8.104 18159 Z= 0.298 Chirality : 0.044 0.175 2087 Planarity : 0.004 0.038 2251 Dihedral : 14.318 164.168 1993 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.28 % Allowed : 20.97 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1556 helix: 3.52 (0.21), residues: 501 sheet: -0.73 (0.26), residues: 410 loop : -1.61 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.009 0.001 TYR A 102 PHE 0.019 0.001 PHE D 106 TRP 0.008 0.001 TRP C 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00356 (13334) covalent geometry : angle 0.57380 (18159) hydrogen bonds : bond 0.06022 ( 571) hydrogen bonds : angle 4.95717 ( 1754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 154 ASP cc_start: 0.7730 (m-30) cc_final: 0.6885 (t0) outliers start: 32 outliers final: 22 residues processed: 213 average time/residue: 0.0978 time to fit residues: 30.9012 Evaluate side-chains 204 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 200 ASN C 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118022 restraints weight = 30201.352| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.45 r_work: 0.2940 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13334 Z= 0.109 Angle : 0.539 8.793 18159 Z= 0.279 Chirality : 0.043 0.167 2087 Planarity : 0.004 0.034 2251 Dihedral : 13.812 163.065 1993 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.85 % Allowed : 21.83 % Favored : 76.32 % 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: 0.69 (0.22), residues: 1556 helix: 3.67 (0.21), residues: 502 sheet: -0.57 (0.26), residues: 407 loop : -1.55 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.025 0.001 TYR D 102 PHE 0.016 0.001 PHE D 116 TRP 0.005 0.001 TRP D 160 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00237 (13334) covalent geometry : angle 0.53935 (18159) hydrogen bonds : bond 0.04806 ( 571) hydrogen bonds : angle 4.46853 ( 1754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.497 Fit side-chains REVERT: A 26 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: E 197 TYR cc_start: 0.9210 (m-80) cc_final: 0.8912 (m-80) REVERT: B 154 ASP cc_start: 0.7866 (m-30) cc_final: 0.6992 (t0) REVERT: B 170 LYS cc_start: 0.7022 (tppt) cc_final: 0.6757 (tptp) outliers start: 26 outliers final: 17 residues processed: 225 average time/residue: 0.0944 time to fit residues: 31.6010 Evaluate side-chains 206 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 27 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 74 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 0.0870 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN B 200 ASN C 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107014 restraints weight = 28672.415| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.32 r_work: 0.2838 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13334 Z= 0.184 Angle : 0.583 7.989 18159 Z= 0.301 Chirality : 0.044 0.170 2087 Planarity : 0.004 0.040 2251 Dihedral : 13.789 168.896 1993 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.92 % Allowed : 21.90 % Favored : 75.18 % 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: 0.60 (0.22), residues: 1556 helix: 3.50 (0.21), residues: 500 sheet: -0.50 (0.26), residues: 403 loop : -1.58 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.020 0.001 TYR D 102 PHE 0.018 0.001 PHE D 106 TRP 0.007 0.001 TRP E 213 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00452 (13334) covalent geometry : angle 0.58263 (18159) hydrogen bonds : bond 0.06521 ( 571) hydrogen bonds : angle 4.58022 ( 1754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.428 Fit side-chains REVERT: A 26 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: E 131 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8844 (tt) REVERT: B 154 ASP cc_start: 0.7870 (m-30) cc_final: 0.6926 (t0) outliers start: 41 outliers final: 34 residues processed: 215 average time/residue: 0.0909 time to fit residues: 29.5375 Evaluate side-chains 216 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN C 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115249 restraints weight = 21800.434| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.82 r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13334 Z= 0.137 Angle : 0.556 8.671 18159 Z= 0.287 Chirality : 0.043 0.166 2087 Planarity : 0.004 0.039 2251 Dihedral : 13.587 176.715 1993 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.28 % Allowed : 21.90 % Favored : 74.82 % 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: 0.69 (0.22), residues: 1556 helix: 3.57 (0.21), residues: 500 sheet: -0.47 (0.26), residues: 401 loop : -1.51 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.032 0.001 TYR B 102 PHE 0.020 0.001 PHE E 54 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00324 (13334) covalent geometry : angle 0.55570 (18159) hydrogen bonds : bond 0.05728 ( 571) hydrogen bonds : angle 4.40729 ( 1754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.453 Fit side-chains REVERT: A 26 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6764 (mm-30) REVERT: E 40 ASN cc_start: 0.8161 (p0) cc_final: 0.7923 (p0) REVERT: E 64 LYS cc_start: 0.5376 (ptpt) cc_final: 0.4857 (mtmt) REVERT: B 54 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6553 (t80) REVERT: B 154 ASP cc_start: 0.7748 (m-30) cc_final: 0.6898 (t0) REVERT: B 287 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8134 (mtm-85) outliers start: 46 outliers final: 39 residues processed: 218 average time/residue: 0.0908 time to fit residues: 29.8694 Evaluate side-chains 223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114498 restraints weight = 28689.173| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.42 r_work: 0.2855 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13334 Z= 0.195 Angle : 0.591 8.414 18159 Z= 0.306 Chirality : 0.044 0.169 2087 Planarity : 0.004 0.043 2251 Dihedral : 13.666 179.700 1993 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.71 % Allowed : 21.47 % Favored : 74.82 % 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: 0.58 (0.22), residues: 1556 helix: 3.43 (0.21), residues: 500 sheet: -0.50 (0.26), residues: 401 loop : -1.55 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.026 0.001 TYR B 102 PHE 0.019 0.001 PHE D 106 TRP 0.006 0.001 TRP E 213 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00482 (13334) covalent geometry : angle 0.59143 (18159) hydrogen bonds : bond 0.06611 ( 571) hydrogen bonds : angle 4.52114 ( 1754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.401 Fit side-chains REVERT: A 26 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: E 131 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8833 (tt) REVERT: B 54 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6549 (t80) REVERT: B 154 ASP cc_start: 0.7854 (m-30) cc_final: 0.6933 (t0) REVERT: B 287 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8229 (mtm-85) outliers start: 52 outliers final: 43 residues processed: 220 average time/residue: 0.0959 time to fit residues: 31.9889 Evaluate side-chains 230 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104696 restraints weight = 35911.000| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.70 r_work: 0.2853 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13334 Z= 0.148 Angle : 0.570 8.564 18159 Z= 0.294 Chirality : 0.044 0.164 2087 Planarity : 0.004 0.042 2251 Dihedral : 13.500 177.753 1993 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.71 % Allowed : 21.75 % Favored : 74.54 % 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: 0.66 (0.22), residues: 1556 helix: 3.52 (0.21), residues: 500 sheet: -0.45 (0.26), residues: 403 loop : -1.54 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.029 0.001 TYR B 102 PHE 0.016 0.001 PHE D 116 TRP 0.006 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00353 (13334) covalent geometry : angle 0.57034 (18159) hydrogen bonds : bond 0.06011 ( 571) hydrogen bonds : angle 4.39655 ( 1754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.402 Fit side-chains REVERT: A 26 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: E 131 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8855 (tt) REVERT: B 54 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6559 (t80) REVERT: B 154 ASP cc_start: 0.7915 (m-30) cc_final: 0.6959 (t0) REVERT: B 287 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8225 (mtm-85) outliers start: 52 outliers final: 45 residues processed: 226 average time/residue: 0.0924 time to fit residues: 31.6891 Evaluate side-chains 233 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113668 restraints weight = 29368.543| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.63 r_work: 0.2872 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13334 Z= 0.112 Angle : 0.547 9.791 18159 Z= 0.281 Chirality : 0.043 0.159 2087 Planarity : 0.004 0.042 2251 Dihedral : 12.997 176.875 1993 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.71 % Allowed : 23.04 % Favored : 74.25 % 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: 0.85 (0.22), residues: 1556 helix: 3.75 (0.20), residues: 496 sheet: -0.40 (0.26), residues: 403 loop : -1.40 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.029 0.001 TYR B 102 PHE 0.022 0.001 PHE D 106 TRP 0.006 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00242 (13334) covalent geometry : angle 0.54715 (18159) hydrogen bonds : bond 0.04699 ( 571) hydrogen bonds : angle 4.13487 ( 1754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.448 Fit side-chains REVERT: E 7 PRO cc_start: 0.7839 (Cg_exo) cc_final: 0.7617 (Cg_endo) REVERT: E 197 TYR cc_start: 0.9177 (m-80) cc_final: 0.8886 (m-80) REVERT: B 54 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6581 (t80) REVERT: B 154 ASP cc_start: 0.7885 (m-30) cc_final: 0.6948 (t0) REVERT: B 252 MET cc_start: 0.8064 (tpt) cc_final: 0.7635 (tpt) REVERT: B 282 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6752 (tm-30) outliers start: 38 outliers final: 33 residues processed: 220 average time/residue: 0.0918 time to fit residues: 30.6303 Evaluate side-chains 215 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107127 restraints weight = 26338.097| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.20 r_work: 0.2865 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13334 Z= 0.149 Angle : 0.571 8.685 18159 Z= 0.293 Chirality : 0.044 0.163 2087 Planarity : 0.004 0.040 2251 Dihedral : 12.986 176.762 1993 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.92 % Allowed : 23.54 % Favored : 73.54 % 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: 0.82 (0.22), residues: 1556 helix: 3.68 (0.20), residues: 496 sheet: -0.41 (0.26), residues: 403 loop : -1.40 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.026 0.001 TYR B 102 PHE 0.022 0.001 PHE A 312 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00360 (13334) covalent geometry : angle 0.57058 (18159) hydrogen bonds : bond 0.05399 ( 571) hydrogen bonds : angle 4.21152 ( 1754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.370 Fit side-chains REVERT: E 7 PRO cc_start: 0.7809 (Cg_exo) cc_final: 0.7591 (Cg_endo) REVERT: E 197 TYR cc_start: 0.9198 (m-80) cc_final: 0.8915 (m-80) REVERT: B 54 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6570 (t80) REVERT: B 154 ASP cc_start: 0.7905 (m-30) cc_final: 0.6948 (t0) REVERT: B 252 MET cc_start: 0.8003 (tpt) cc_final: 0.7571 (tpt) REVERT: B 282 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6837 (tm-30) REVERT: B 287 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8195 (mtm-85) outliers start: 41 outliers final: 37 residues processed: 213 average time/residue: 0.0957 time to fit residues: 31.0057 Evaluate side-chains 219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 0.0050 chunk 142 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111273 restraints weight = 31915.007| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.65 r_work: 0.2861 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13334 Z= 0.123 Angle : 0.562 9.091 18159 Z= 0.288 Chirality : 0.043 0.160 2087 Planarity : 0.004 0.043 2251 Dihedral : 12.851 176.281 1993 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.71 % Allowed : 23.61 % Favored : 73.68 % 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 (0.22), residues: 1556 helix: 3.74 (0.20), residues: 496 sheet: -0.36 (0.26), residues: 403 loop : -1.38 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.027 0.001 TYR B 102 PHE 0.022 0.001 PHE D 106 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00282 (13334) covalent geometry : angle 0.56153 (18159) hydrogen bonds : bond 0.05063 ( 571) hydrogen bonds : angle 4.14822 ( 1754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.422 Fit side-chains REVERT: E 197 TYR cc_start: 0.9200 (m-80) cc_final: 0.8908 (m-80) REVERT: B 54 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6571 (t80) REVERT: B 154 ASP cc_start: 0.7937 (m-30) cc_final: 0.6959 (t0) REVERT: B 252 MET cc_start: 0.8030 (tpt) cc_final: 0.7600 (tpt) REVERT: B 282 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6790 (tm-30) REVERT: B 287 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8124 (mtm-85) outliers start: 38 outliers final: 35 residues processed: 209 average time/residue: 0.1039 time to fit residues: 32.7765 Evaluate side-chains 218 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 312 PHE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 40 optimal weight: 0.0870 chunk 135 optimal weight: 0.0870 chunk 15 optimal weight: 7.9990 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107332 restraints weight = 25136.566| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.24 r_work: 0.2892 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13334 Z= 0.120 Angle : 0.561 9.014 18159 Z= 0.287 Chirality : 0.043 0.159 2087 Planarity : 0.004 0.043 2251 Dihedral : 12.725 176.107 1993 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.00 % Allowed : 23.47 % Favored : 73.54 % 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: 0.91 (0.22), residues: 1556 helix: 3.76 (0.20), residues: 496 sheet: -0.33 (0.26), residues: 403 loop : -1.36 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.027 0.001 TYR B 102 PHE 0.018 0.001 PHE E 54 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00276 (13334) covalent geometry : angle 0.56078 (18159) hydrogen bonds : bond 0.04909 ( 571) hydrogen bonds : angle 4.11166 ( 1754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.00 seconds wall clock time: 51 minutes 15.47 seconds (3075.47 seconds total)