Starting phenix.real_space_refine on Fri Aug 7 08:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmz_51458/08_2026/9gmz_51458.cif" } resolution = 3.2 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12902 2.51 5 N 3571 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20472 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2688 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "C" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "G" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "1" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.69, per 1000 atoms: 0.23 Number of scatterers: 20472 At special positions: 0 Unit cell: (97.5, 150.8, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 51 15.00 Mg 7 11.99 O 3885 8.00 N 3571 7.00 C 12902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 755.5 milliseconds 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4604 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 10 sheets defined 63.3% alpha, 6.7% beta 16 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 62 through 85 Proline residue: A 80 - end of helix removed outlier: 4.102A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.209A pdb=" N GLN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.377A pdb=" N PHE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.798A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.665A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 62 through 83 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.575A pdb=" N HIS B 124 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 200 removed outlier: 4.279A pdb=" N ASP B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.831A pdb=" N THR B 213 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 237 through 255 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLU C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.250A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 200 removed outlier: 4.114A pdb=" N ASP C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.526A pdb=" N THR C 213 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.821A pdb=" N ARG C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.743A pdb=" N ARG C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.515A pdb=" N LYS C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.612A pdb=" N VAL C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 26 removed outlier: 3.507A pdb=" N ARG D 19 " --> pdb=" O PRO D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 62 through 83 removed outlier: 3.782A pdb=" N LEU D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) Proline residue: D 80 - end of helix removed outlier: 3.900A pdb=" N GLU D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.186A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.694A pdb=" N HIS D 175 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 200 removed outlier: 4.687A pdb=" N ASP D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 237 through 255 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.863A pdb=" N ARG D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.593A pdb=" N ARG D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 121 through 125 removed outlier: 3.766A pdb=" N HIS E 124 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 164 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.937A pdb=" N ASP E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.518A pdb=" N THR E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 237 through 254 Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 266 through 275 Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.700A pdb=" N ARG E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.575A pdb=" N ARG E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.583A pdb=" N VAL E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.504A pdb=" N GLU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.138A pdb=" N GLU F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.795A pdb=" N TYR F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 125 Processing helix chain 'F' and resid 148 through 164 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.889A pdb=" N ASP F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 4.005A pdb=" N THR F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 Processing helix chain 'F' and resid 237 through 253 Processing helix chain 'F' and resid 266 through 275 Processing helix chain 'F' and resid 277 through 296 Processing helix chain 'F' and resid 301 through 308 removed outlier: 4.024A pdb=" N ARG F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 328 removed outlier: 3.953A pdb=" N GLN F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 62 through 83 Proline residue: G 80 - end of helix Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 121 through 125 removed outlier: 3.959A pdb=" N HIS G 124 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.610A pdb=" N LEU G 211 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR G 213 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 237 through 255 Processing helix chain 'G' and resid 262 through 265 Processing helix chain 'G' and resid 266 through 275 Processing helix chain 'G' and resid 277 through 296 Processing helix chain 'G' and resid 301 through 308 removed outlier: 4.055A pdb=" N ARG G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 330 Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.500A pdb=" N VAL G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.770A pdb=" N VAL A 92 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP A 171 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 94 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 168 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 206 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 170 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 53 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY A 207 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 55 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.776A pdb=" N VAL B 92 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP B 171 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE B 94 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 168 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 206 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 170 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE B 53 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY B 207 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 55 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 52 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 228 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 54 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 230 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 56 " --> pdb=" O PHE B 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.517A pdb=" N VAL C 92 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 168 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 206 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 170 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.556A pdb=" N SER C 134 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.752A pdb=" N VAL D 92 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP D 171 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 94 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE D 168 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 206 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 170 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE D 53 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY D 207 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL D 55 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE D 52 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE D 228 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE D 54 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D 230 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR D 56 " --> pdb=" O PHE D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.543A pdb=" N VAL E 92 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP E 171 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 94 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 53 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY E 207 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 55 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 removed outlier: 3.601A pdb=" N SER E 134 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.833A pdb=" N VAL F 92 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP F 171 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 94 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE F 168 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU F 206 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL F 170 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE F 53 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 207 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 55 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE F 52 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE F 228 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE F 54 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE F 230 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR F 56 " --> pdb=" O PHE F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 95 removed outlier: 6.583A pdb=" N VAL G 92 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP G 171 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE G 94 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE G 168 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU G 206 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL G 170 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE G 53 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY G 207 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 55 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE G 52 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE G 228 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE G 54 " --> pdb=" O ILE G 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1038 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3318 1.31 - 1.44: 5746 1.44 - 1.56: 11719 1.56 - 1.68: 81 1.68 - 1.81: 91 Bond restraints: 20955 Sorted by residual: bond pdb=" CA GLU D 172 " pdb=" C GLU D 172 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.17e-02 7.31e+03 3.93e+01 bond pdb=" CA TYR B 271 " pdb=" C TYR B 271 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.29e-02 6.01e+03 2.51e+01 bond pdb=" CA GLU B 272 " pdb=" C GLU B 272 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.25e+01 bond pdb=" CA VAL K 893 " pdb=" C VAL K 893 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.04e-02 9.25e+03 1.39e+01 bond pdb=" CA ASN G 105 " pdb=" C ASN G 105 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.27e-02 6.20e+03 1.22e+01 ... (remaining 20950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28139 2.33 - 4.66: 346 4.66 - 6.99: 33 6.99 - 9.32: 20 9.32 - 11.65: 6 Bond angle restraints: 28544 Sorted by residual: angle pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" C VAL E 61 " ideal model delta sigma weight residual 110.72 119.36 -8.64 1.01e+00 9.80e-01 7.32e+01 angle pdb=" N ARG D 215 " pdb=" CA ARG D 215 " pdb=" C ARG D 215 " ideal model delta sigma weight residual 111.40 120.18 -8.78 1.22e+00 6.72e-01 5.18e+01 angle pdb=" N VAL L 893 " pdb=" CA VAL L 893 " pdb=" C VAL L 893 " ideal model delta sigma weight residual 108.11 117.83 -9.72 1.40e+00 5.10e-01 4.83e+01 angle pdb=" N VAL J 893 " pdb=" CA VAL J 893 " pdb=" C VAL J 893 " ideal model delta sigma weight residual 108.11 115.99 -7.88 1.40e+00 5.10e-01 3.17e+01 angle pdb=" N PRO G 90 " pdb=" CA PRO G 90 " pdb=" C PRO G 90 " ideal model delta sigma weight residual 113.53 121.07 -7.54 1.39e+00 5.18e-01 2.94e+01 ... (remaining 28539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 11426 23.07 - 46.15: 985 46.15 - 69.22: 187 69.22 - 92.29: 35 92.29 - 115.37: 3 Dihedral angle restraints: 12636 sinusoidal: 5515 harmonic: 7121 Sorted by residual: dihedral pdb=" CA THR G 116 " pdb=" C THR G 116 " pdb=" N LEU G 117 " pdb=" CA LEU G 117 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C VAL E 61 " pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" CB VAL E 61 " ideal model delta harmonic sigma weight residual -122.00 -132.61 10.61 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C VAL C 61 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " pdb=" CB VAL C 61 " ideal model delta harmonic sigma weight residual -122.00 -131.88 9.88 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 12633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2951 0.087 - 0.174: 225 0.174 - 0.261: 11 0.261 - 0.348: 7 0.348 - 0.435: 3 Chirality restraints: 3197 Sorted by residual: chirality pdb=" CA ARG C 340 " pdb=" N ARG C 340 " pdb=" C ARG C 340 " pdb=" CB ARG C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA PRO G 90 " pdb=" N PRO G 90 " pdb=" C PRO G 90 " pdb=" CB PRO G 90 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ALA G 98 " pdb=" N ALA G 98 " pdb=" C ALA G 98 " pdb=" CB ALA G 98 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3194 not shown) Planarity restraints: 3523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 101 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C SER C 101 " 0.080 2.00e-02 2.50e+03 pdb=" O SER C 101 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG C 102 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 98 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO G 99 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 99 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 99 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 126 " 0.018 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE G 126 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE G 126 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE G 126 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE G 126 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE G 126 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 3520 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 145 2.52 - 3.11: 15279 3.11 - 3.71: 33283 3.71 - 4.30: 45166 4.30 - 4.90: 75082 Nonbonded interactions: 168955 Sorted by model distance: nonbonded pdb=" O1B ANP C 401 " pdb="MG MG C 402 " model vdw 1.922 2.170 nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 1.941 2.170 nonbonded pdb=" O1G ANP F 401 " pdb="MG MG F 402 " model vdw 1.972 2.170 nonbonded pdb=" O1B ANP B 401 " pdb="MG MG B 402 " model vdw 1.998 2.170 nonbonded pdb=" O1B ANP D 401 " pdb="MG MG D 402 " model vdw 2.016 2.170 ... (remaining 168950 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 '1' and resid 1 through 14) selection = (chain '2' and ((resid -14 and (name C4' or name O4' or name C3' or name O3' or \ name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 or n \ ame N6 or name N1 or name C2 or name N3 or name C4 )) or resid -13 through -1)) } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 337 or resid 401 through 402)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.480 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20955 Z= 0.249 Angle : 0.654 11.650 28544 Z= 0.398 Chirality : 0.047 0.435 3197 Planarity : 0.004 0.078 3523 Dihedral : 17.085 115.366 8032 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.38 % Allowed : 14.42 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2407 helix: 1.71 (0.14), residues: 1430 sheet: 0.44 (0.40), residues: 196 loop : 0.29 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.034 0.001 TYR G 110 PHE 0.038 0.001 PHE G 126 TRP 0.006 0.001 TRP C 284 HIS 0.003 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.25 (20955) covalent geometry : angle 0.65448 / 0.40 (28544) hydrogen bonds : bond 0.16020 / 10.12 ( 1078) hydrogen bonds : angle 4.63898 / 3.37 ( 2933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8586 (p90) cc_final: 0.8171 (t80) REVERT: A 142 ASN cc_start: 0.8021 (m110) cc_final: 0.7586 (m110) REVERT: A 164 HIS cc_start: 0.8787 (t-90) cc_final: 0.8097 (t-90) REVERT: A 198 MET cc_start: 0.8051 (mtm) cc_final: 0.7653 (ptp) REVERT: A 267 TRP cc_start: 0.9008 (p-90) cc_final: 0.8725 (p-90) REVERT: A 328 GLN cc_start: 0.8299 (mt0) cc_final: 0.8012 (mp10) REVERT: B 35 GLU cc_start: 0.8851 (tt0) cc_final: 0.8461 (tm-30) REVERT: B 73 LYS cc_start: 0.9019 (tptm) cc_final: 0.8624 (tppt) REVERT: B 227 ASP cc_start: 0.8832 (m-30) cc_final: 0.8353 (p0) REVERT: C 34 LYS cc_start: 0.9324 (mmmt) cc_final: 0.8887 (mtpt) REVERT: C 69 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8072 (tpp80) REVERT: C 121 LEU cc_start: 0.8937 (mp) cc_final: 0.8579 (pp) REVERT: C 137 ASN cc_start: 0.8956 (t0) cc_final: 0.8588 (t0) REVERT: C 198 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: C 307 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8649 (mmtp) REVERT: D 14 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8158 (mmm160) REVERT: D 24 GLU cc_start: 0.9304 (tp30) cc_final: 0.8954 (tp30) REVERT: D 164 HIS cc_start: 0.8239 (t-170) cc_final: 0.7888 (t-170) REVERT: E 56 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7633 (p90) REVERT: E 94 ILE cc_start: 0.9051 (tp) cc_final: 0.8761 (pt) REVERT: E 102 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7320 (ttp-110) REVERT: E 103 TYR cc_start: 0.7912 (p90) cc_final: 0.7654 (p90) REVERT: E 262 ASN cc_start: 0.8798 (t0) cc_final: 0.8389 (t0) REVERT: F 119 GLU cc_start: 0.6618 (tp30) cc_final: 0.6356 (pt0) REVERT: F 140 LYS cc_start: 0.7522 (ptpt) cc_final: 0.6534 (tmmt) REVERT: F 142 ASN cc_start: 0.9288 (p0) cc_final: 0.8584 (p0) REVERT: G 41 MET cc_start: 0.9349 (tpt) cc_final: 0.9079 (tpt) REVERT: G 198 MET cc_start: 0.9200 (mtm) cc_final: 0.8876 (mtm) REVERT: G 270 PHE cc_start: 0.8821 (m-80) cc_final: 0.8557 (m-80) REVERT: G 271 TYR cc_start: 0.7656 (t80) cc_final: 0.7303 (t80) REVERT: G 303 LYS cc_start: 0.9094 (tppt) cc_final: 0.8871 (mmtp) REVERT: H 898 PHE cc_start: 0.6818 (t80) cc_final: 0.6427 (t80) outliers start: 29 outliers final: 14 residues processed: 190 average time/residue: 0.1467 time to fit residues: 43.2135 Evaluate side-chains 158 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS D 242 GLN E 216 ASN E 242 GLN G 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.056295 restraints weight = 56896.721| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.65 r_work: 0.2808 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20955 Z= 0.224 Angle : 0.620 9.464 28544 Z= 0.312 Chirality : 0.043 0.221 3197 Planarity : 0.005 0.059 3523 Dihedral : 13.420 118.010 3301 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 14.52 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 2407 helix: 1.47 (0.14), residues: 1472 sheet: 0.28 (0.39), residues: 196 loop : 0.42 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.015 0.001 TYR A 103 PHE 0.025 0.002 PHE D 319 TRP 0.012 0.001 TRP C 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (20955) covalent geometry : angle 0.62047 / 0.31 (28544) hydrogen bonds : bond 0.04478 / 2.93 ( 1078) hydrogen bonds : angle 4.05066 / 2.91 ( 2933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8542 (p90) cc_final: 0.8121 (t80) REVERT: A 142 ASN cc_start: 0.8081 (m110) cc_final: 0.7626 (m110) REVERT: A 164 HIS cc_start: 0.8724 (t-90) cc_final: 0.7986 (t-90) REVERT: A 198 MET cc_start: 0.7970 (mtm) cc_final: 0.7504 (ptp) REVERT: A 328 GLN cc_start: 0.8314 (mt0) cc_final: 0.8044 (mp10) REVERT: B 35 GLU cc_start: 0.8927 (tt0) cc_final: 0.8560 (tm-30) REVERT: B 73 LYS cc_start: 0.9074 (tptm) cc_final: 0.8634 (tppt) REVERT: B 137 ASN cc_start: 0.7847 (t0) cc_final: 0.7371 (p0) REVERT: B 220 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7709 (tp40) REVERT: B 227 ASP cc_start: 0.8823 (m-30) cc_final: 0.8400 (p0) REVERT: C 34 LYS cc_start: 0.9334 (mmmt) cc_final: 0.8970 (mtpt) REVERT: C 121 LEU cc_start: 0.8931 (mp) cc_final: 0.8612 (pp) REVERT: C 137 ASN cc_start: 0.8945 (t0) cc_final: 0.8516 (p0) REVERT: C 198 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: C 221 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 307 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8885 (tppt) REVERT: D 24 GLU cc_start: 0.9355 (tp30) cc_final: 0.8972 (tp30) REVERT: E 56 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7772 (p90) REVERT: E 102 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.7469 (ttp-110) REVERT: E 103 TYR cc_start: 0.8029 (p90) cc_final: 0.7764 (p90) REVERT: E 105 ASN cc_start: 0.9094 (t0) cc_final: 0.8842 (t0) REVERT: E 210 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8575 (mp0) REVERT: E 262 ASN cc_start: 0.8789 (t0) cc_final: 0.8463 (t0) REVERT: F 119 GLU cc_start: 0.6704 (tp30) cc_final: 0.6465 (pt0) REVERT: F 140 LYS cc_start: 0.7564 (ptpt) cc_final: 0.6610 (tmmt) REVERT: F 142 ASN cc_start: 0.9301 (p0) cc_final: 0.8495 (p0) REVERT: F 172 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7956 (mt-10) REVERT: G 41 MET cc_start: 0.9369 (tpt) cc_final: 0.9095 (tpt) REVERT: G 271 TYR cc_start: 0.7918 (t80) cc_final: 0.7563 (t80) REVERT: H 898 PHE cc_start: 0.7122 (t80) cc_final: 0.6754 (t80) REVERT: I 893 VAL cc_start: 0.8317 (t) cc_final: 0.8011 (p) REVERT: J 895 TYR cc_start: 0.8766 (m-80) cc_final: 0.8502 (m-80) REVERT: M 893 VAL cc_start: 0.8330 (m) cc_final: 0.8112 (p) outliers start: 52 outliers final: 24 residues processed: 184 average time/residue: 0.1593 time to fit residues: 44.8888 Evaluate side-chains 164 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057355 restraints weight = 56066.724| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.61 r_work: 0.2806 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20955 Z= 0.121 Angle : 0.512 8.693 28544 Z= 0.260 Chirality : 0.040 0.165 3197 Planarity : 0.004 0.058 3523 Dihedral : 13.197 113.980 3287 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.19 % Allowed : 15.04 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.18), residues: 2407 helix: 1.61 (0.14), residues: 1465 sheet: 0.18 (0.40), residues: 196 loop : 0.51 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 14 TYR 0.028 0.001 TYR G 110 PHE 0.015 0.001 PHE D 126 TRP 0.009 0.001 TRP F 284 HIS 0.003 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (20955) covalent geometry : angle 0.51217 / 0.26 (28544) hydrogen bonds : bond 0.04077 / 2.67 ( 1078) hydrogen bonds : angle 3.72451 / 2.67 ( 2933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8474 (p90) cc_final: 0.8136 (t80) REVERT: A 142 ASN cc_start: 0.8092 (m110) cc_final: 0.7630 (m110) REVERT: A 164 HIS cc_start: 0.8761 (t-90) cc_final: 0.8013 (t-90) REVERT: A 198 MET cc_start: 0.7944 (mtm) cc_final: 0.7447 (ptp) REVERT: A 328 GLN cc_start: 0.8315 (mt0) cc_final: 0.8039 (mp10) REVERT: B 73 LYS cc_start: 0.9067 (tptm) cc_final: 0.8642 (tppt) REVERT: B 137 ASN cc_start: 0.7808 (t0) cc_final: 0.7442 (p0) REVERT: B 227 ASP cc_start: 0.8808 (m-30) cc_final: 0.8373 (p0) REVERT: C 34 LYS cc_start: 0.9337 (mmmt) cc_final: 0.8973 (mtpt) REVERT: C 121 LEU cc_start: 0.8891 (mp) cc_final: 0.8557 (pp) REVERT: C 137 ASN cc_start: 0.8965 (t0) cc_final: 0.8577 (t0) REVERT: C 307 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8900 (tppt) REVERT: D 14 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8368 (mmm160) REVERT: D 24 GLU cc_start: 0.9328 (tp30) cc_final: 0.8928 (tp30) REVERT: E 56 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7767 (p90) REVERT: E 102 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7532 (ttp-110) REVERT: E 103 TYR cc_start: 0.7956 (p90) cc_final: 0.7723 (p90) REVERT: E 105 ASN cc_start: 0.9104 (t0) cc_final: 0.8859 (t0) REVERT: E 131 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8224 (mtm110) REVERT: E 262 ASN cc_start: 0.8771 (t0) cc_final: 0.8435 (t0) REVERT: F 92 VAL cc_start: 0.9273 (t) cc_final: 0.8962 (p) REVERT: F 140 LYS cc_start: 0.7566 (ptpt) cc_final: 0.6612 (tmmt) REVERT: F 142 ASN cc_start: 0.9298 (p0) cc_final: 0.8502 (p0) REVERT: F 172 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7883 (mt-10) REVERT: G 41 MET cc_start: 0.9370 (tpt) cc_final: 0.9081 (tpt) REVERT: G 131 ARG cc_start: 0.8348 (ppt170) cc_final: 0.8008 (tmt170) REVERT: G 271 TYR cc_start: 0.7860 (t80) cc_final: 0.7520 (t80) REVERT: H 898 PHE cc_start: 0.7174 (t80) cc_final: 0.6841 (t80) REVERT: I 893 VAL cc_start: 0.8423 (t) cc_final: 0.8138 (p) REVERT: I 897 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7370 (tp30) REVERT: K 895 TYR cc_start: 0.8908 (m-80) cc_final: 0.8645 (m-80) REVERT: L 897 GLU cc_start: 0.9224 (tt0) cc_final: 0.8826 (tt0) outliers start: 46 outliers final: 21 residues processed: 177 average time/residue: 0.1535 time to fit residues: 42.3623 Evaluate side-chains 155 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 chunk 237 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN G 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056654 restraints weight = 56371.925| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.64 r_work: 0.2793 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20955 Z= 0.129 Angle : 0.504 7.372 28544 Z= 0.254 Chirality : 0.040 0.177 3197 Planarity : 0.004 0.053 3523 Dihedral : 13.139 114.477 3284 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.28 % Allowed : 15.37 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.18), residues: 2407 helix: 1.65 (0.14), residues: 1465 sheet: 0.11 (0.39), residues: 196 loop : 0.57 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.027 0.001 TYR G 110 PHE 0.015 0.001 PHE F 138 TRP 0.008 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20955) covalent geometry : angle 0.50381 / 0.25 (28544) hydrogen bonds : bond 0.03736 / 2.46 ( 1078) hydrogen bonds : angle 3.62159 / 2.59 ( 2933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8448 (p90) cc_final: 0.8139 (t80) REVERT: A 142 ASN cc_start: 0.8128 (m110) cc_final: 0.7665 (m110) REVERT: A 164 HIS cc_start: 0.8788 (t-90) cc_final: 0.8094 (t-90) REVERT: A 198 MET cc_start: 0.7976 (mtm) cc_final: 0.7475 (ptp) REVERT: A 328 GLN cc_start: 0.8315 (mt0) cc_final: 0.8052 (mp10) REVERT: B 73 LYS cc_start: 0.9070 (tptm) cc_final: 0.8633 (tppt) REVERT: B 137 ASN cc_start: 0.7822 (t0) cc_final: 0.7510 (p0) REVERT: B 227 ASP cc_start: 0.8801 (m-30) cc_final: 0.8385 (p0) REVERT: C 34 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8907 (mtpt) REVERT: C 121 LEU cc_start: 0.8888 (mp) cc_final: 0.8557 (pp) REVERT: C 137 ASN cc_start: 0.8962 (t0) cc_final: 0.8556 (p0) REVERT: C 221 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8877 (mm) REVERT: D 24 GLU cc_start: 0.9337 (tp30) cc_final: 0.8943 (tp30) REVERT: D 41 MET cc_start: 0.8987 (mmm) cc_final: 0.8745 (mmm) REVERT: D 142 ASN cc_start: 0.9086 (m-40) cc_final: 0.8198 (p0) REVERT: E 56 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7751 (p90) REVERT: E 102 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7578 (ttp-110) REVERT: E 103 TYR cc_start: 0.7941 (p90) cc_final: 0.7736 (p90) REVERT: E 262 ASN cc_start: 0.8805 (t0) cc_final: 0.8483 (t0) REVERT: F 92 VAL cc_start: 0.9279 (t) cc_final: 0.8982 (p) REVERT: F 140 LYS cc_start: 0.7562 (ptpt) cc_final: 0.6611 (tmmt) REVERT: F 142 ASN cc_start: 0.9302 (p0) cc_final: 0.8505 (p0) REVERT: F 172 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7894 (mt-10) REVERT: G 41 MET cc_start: 0.9385 (tpt) cc_final: 0.9094 (tpt) REVERT: G 68 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9215 (mm) REVERT: G 131 ARG cc_start: 0.8367 (ppt170) cc_final: 0.8002 (tmt170) REVERT: G 271 TYR cc_start: 0.7839 (t80) cc_final: 0.7515 (t80) REVERT: H 898 PHE cc_start: 0.7259 (t80) cc_final: 0.6997 (t80) REVERT: I 893 VAL cc_start: 0.8585 (t) cc_final: 0.8328 (p) REVERT: I 897 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7440 (tp30) REVERT: K 895 TYR cc_start: 0.8920 (m-80) cc_final: 0.8705 (m-80) REVERT: K 896 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8251 (tt0) outliers start: 48 outliers final: 27 residues processed: 179 average time/residue: 0.1516 time to fit residues: 42.7070 Evaluate side-chains 161 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 67 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN D 203 HIS E 216 ASN F 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054384 restraints weight = 56751.646| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.61 r_work: 0.2761 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20955 Z= 0.201 Angle : 0.568 10.515 28544 Z= 0.282 Chirality : 0.042 0.222 3197 Planarity : 0.004 0.048 3523 Dihedral : 13.184 112.988 3277 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.09 % Allowed : 15.23 % Favored : 81.68 % 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: 1.57 (0.18), residues: 2407 helix: 1.59 (0.14), residues: 1467 sheet: 0.00 (0.40), residues: 196 loop : 0.42 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 69 TYR 0.029 0.001 TYR G 110 PHE 0.015 0.002 PHE D 23 TRP 0.013 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (20955) covalent geometry : angle 0.56764 / 0.28 (28544) hydrogen bonds : bond 0.04018 / 2.64 ( 1078) hydrogen bonds : angle 3.69298 / 2.65 ( 2933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8494 (p90) cc_final: 0.8152 (t80) REVERT: A 142 ASN cc_start: 0.8130 (m110) cc_final: 0.7682 (m110) REVERT: A 164 HIS cc_start: 0.8805 (t-90) cc_final: 0.8097 (t-90) REVERT: A 198 MET cc_start: 0.7957 (mtm) cc_final: 0.7439 (ptp) REVERT: A 328 GLN cc_start: 0.8292 (mt0) cc_final: 0.8044 (mp10) REVERT: B 73 LYS cc_start: 0.9074 (tptm) cc_final: 0.8627 (tppt) REVERT: B 137 ASN cc_start: 0.7855 (t0) cc_final: 0.7576 (p0) REVERT: B 184 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5361 (tmtt) REVERT: B 185 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 227 ASP cc_start: 0.8832 (m-30) cc_final: 0.8404 (p0) REVERT: C 34 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9006 (mtpt) REVERT: C 121 LEU cc_start: 0.8900 (mp) cc_final: 0.8614 (pp) REVERT: C 137 ASN cc_start: 0.8971 (t0) cc_final: 0.8636 (t0) REVERT: C 221 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8870 (mm) REVERT: D 24 GLU cc_start: 0.9369 (tp30) cc_final: 0.8950 (tp30) REVERT: D 142 ASN cc_start: 0.9102 (m-40) cc_final: 0.8158 (p0) REVERT: E 56 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7837 (p90) REVERT: E 105 ASN cc_start: 0.9196 (t0) cc_final: 0.8904 (t0) REVERT: E 210 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8650 (mp0) REVERT: E 262 ASN cc_start: 0.8782 (t0) cc_final: 0.8546 (t0) REVERT: F 92 VAL cc_start: 0.9253 (t) cc_final: 0.8954 (p) REVERT: F 140 LYS cc_start: 0.7566 (ptpt) cc_final: 0.6642 (tmmt) REVERT: F 142 ASN cc_start: 0.9315 (p0) cc_final: 0.8535 (p0) REVERT: F 172 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7932 (mt-10) REVERT: G 68 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9181 (mm) REVERT: G 131 ARG cc_start: 0.8434 (ppt170) cc_final: 0.8051 (tmt170) REVERT: G 176 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7309 (t80) REVERT: I 893 VAL cc_start: 0.8715 (t) cc_final: 0.8486 (p) REVERT: I 897 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7491 (tp30) outliers start: 65 outliers final: 39 residues processed: 190 average time/residue: 0.1445 time to fit residues: 43.6687 Evaluate side-chains 174 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054196 restraints weight = 56353.189| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.59 r_work: 0.2758 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20955 Z= 0.197 Angle : 0.551 9.253 28544 Z= 0.275 Chirality : 0.041 0.194 3197 Planarity : 0.004 0.046 3523 Dihedral : 13.167 109.762 3277 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.76 % Allowed : 15.85 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2407 helix: 1.59 (0.14), residues: 1467 sheet: -0.07 (0.40), residues: 196 loop : 0.37 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.029 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (20955) covalent geometry : angle 0.55086 / 0.27 (28544) hydrogen bonds : bond 0.03897 / 2.57 ( 1078) hydrogen bonds : angle 3.67446 / 2.64 ( 2933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8502 (p90) cc_final: 0.8143 (t80) REVERT: A 142 ASN cc_start: 0.8115 (m110) cc_final: 0.7684 (m110) REVERT: A 164 HIS cc_start: 0.8829 (t-90) cc_final: 0.8132 (t-90) REVERT: A 198 MET cc_start: 0.7885 (mtm) cc_final: 0.7368 (ptp) REVERT: A 215 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7460 (tpt90) REVERT: B 73 LYS cc_start: 0.9067 (tptm) cc_final: 0.8612 (tppt) REVERT: B 137 ASN cc_start: 0.7859 (t0) cc_final: 0.7586 (p0) REVERT: B 227 ASP cc_start: 0.8841 (m-30) cc_final: 0.8418 (p0) REVERT: C 34 LYS cc_start: 0.9345 (mmmt) cc_final: 0.9009 (mtpt) REVERT: C 121 LEU cc_start: 0.8909 (mp) cc_final: 0.8606 (pp) REVERT: C 137 ASN cc_start: 0.9004 (t0) cc_final: 0.8615 (p0) REVERT: C 221 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8886 (mm) REVERT: D 142 ASN cc_start: 0.9094 (m-40) cc_final: 0.8164 (p0) REVERT: D 166 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.9162 (m-30) REVERT: E 56 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7826 (p90) REVERT: E 94 ILE cc_start: 0.8979 (tp) cc_final: 0.8595 (pt) REVERT: E 105 ASN cc_start: 0.9139 (t0) cc_final: 0.8813 (t0) REVERT: F 92 VAL cc_start: 0.9238 (t) cc_final: 0.8929 (p) REVERT: F 140 LYS cc_start: 0.7579 (ptpt) cc_final: 0.6733 (tmmt) REVERT: F 142 ASN cc_start: 0.9295 (p0) cc_final: 0.8815 (p0) REVERT: F 172 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7934 (mt-10) REVERT: G 68 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9171 (mm) REVERT: G 110 TYR cc_start: 0.9198 (m-80) cc_final: 0.8946 (m-80) REVERT: G 131 ARG cc_start: 0.8431 (ppt170) cc_final: 0.8054 (tmt170) REVERT: G 176 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7317 (t80) REVERT: I 893 VAL cc_start: 0.8839 (t) cc_final: 0.8587 (p) REVERT: I 897 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7498 (tp30) outliers start: 58 outliers final: 40 residues processed: 168 average time/residue: 0.1480 time to fit residues: 39.3707 Evaluate side-chains 166 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055590 restraints weight = 56062.966| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.60 r_work: 0.2792 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20955 Z= 0.111 Angle : 0.506 9.847 28544 Z= 0.252 Chirality : 0.039 0.155 3197 Planarity : 0.003 0.043 3523 Dihedral : 13.036 106.732 3277 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.43 % Allowed : 16.18 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2407 helix: 1.78 (0.14), residues: 1452 sheet: -0.06 (0.40), residues: 196 loop : 0.39 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 153 TYR 0.025 0.001 TYR G 110 PHE 0.033 0.001 PHE H 898 TRP 0.007 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20955) covalent geometry : angle 0.50611 / 0.25 (28544) hydrogen bonds : bond 0.03598 / 2.38 ( 1078) hydrogen bonds : angle 3.51521 / 2.52 ( 2933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8482 (p90) cc_final: 0.8182 (t80) REVERT: A 142 ASN cc_start: 0.8143 (m110) cc_final: 0.7715 (m110) REVERT: A 164 HIS cc_start: 0.8841 (t-90) cc_final: 0.8134 (t-90) REVERT: A 198 MET cc_start: 0.7882 (mtm) cc_final: 0.7352 (ptp) REVERT: B 73 LYS cc_start: 0.9046 (tptm) cc_final: 0.8598 (tppt) REVERT: B 137 ASN cc_start: 0.7857 (t0) cc_final: 0.7598 (p0) REVERT: B 227 ASP cc_start: 0.8795 (m-30) cc_final: 0.8452 (p0) REVERT: C 34 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9006 (mtpt) REVERT: C 103 TYR cc_start: 0.8410 (p90) cc_final: 0.7962 (p90) REVERT: C 121 LEU cc_start: 0.8883 (mp) cc_final: 0.8572 (pp) REVERT: C 137 ASN cc_start: 0.8977 (t0) cc_final: 0.8633 (t0) REVERT: C 221 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8892 (mm) REVERT: D 142 ASN cc_start: 0.9087 (m-40) cc_final: 0.8184 (p0) REVERT: E 56 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7806 (p90) REVERT: E 94 ILE cc_start: 0.8992 (tp) cc_final: 0.8654 (pt) REVERT: E 105 ASN cc_start: 0.9156 (t0) cc_final: 0.8797 (t0) REVERT: E 210 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8585 (mp0) REVERT: E 262 ASN cc_start: 0.8807 (t0) cc_final: 0.8602 (t0) REVERT: F 92 VAL cc_start: 0.9248 (t) cc_final: 0.8960 (p) REVERT: F 140 LYS cc_start: 0.7556 (ptpt) cc_final: 0.6663 (tmmt) REVERT: F 142 ASN cc_start: 0.9319 (p0) cc_final: 0.8851 (p0) REVERT: F 172 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7882 (mt-10) REVERT: G 41 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8825 (tpp) REVERT: G 68 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9160 (mm) REVERT: G 110 TYR cc_start: 0.9164 (m-80) cc_final: 0.8920 (m-80) REVERT: G 131 ARG cc_start: 0.8416 (ppt170) cc_final: 0.8036 (tmt170) REVERT: G 176 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7281 (t80) REVERT: I 893 VAL cc_start: 0.8871 (t) cc_final: 0.8645 (p) REVERT: I 897 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7521 (tp30) outliers start: 51 outliers final: 36 residues processed: 171 average time/residue: 0.1487 time to fit residues: 40.0894 Evaluate side-chains 167 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 157 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.078890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.054288 restraints weight = 56779.024| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.59 r_work: 0.2760 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20955 Z= 0.181 Angle : 0.554 10.101 28544 Z= 0.272 Chirality : 0.041 0.254 3197 Planarity : 0.004 0.042 3523 Dihedral : 13.066 106.656 3277 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.28 % Allowed : 16.75 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 2407 helix: 1.77 (0.14), residues: 1452 sheet: -0.10 (0.40), residues: 196 loop : 0.35 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.023 0.001 TYR G 110 PHE 0.023 0.001 PHE H 898 TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (20955) covalent geometry : angle 0.55352 / 0.27 (28544) hydrogen bonds : bond 0.03756 / 2.48 ( 1078) hydrogen bonds : angle 3.57817 / 2.57 ( 2933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8513 (p90) cc_final: 0.8184 (t80) REVERT: A 142 ASN cc_start: 0.8116 (m110) cc_final: 0.7693 (m110) REVERT: A 164 HIS cc_start: 0.8848 (t-90) cc_final: 0.8145 (t-90) REVERT: A 198 MET cc_start: 0.7879 (mtm) cc_final: 0.7353 (ptp) REVERT: B 73 LYS cc_start: 0.9051 (tptm) cc_final: 0.8585 (tppt) REVERT: B 137 ASN cc_start: 0.7897 (t0) cc_final: 0.7628 (p0) REVERT: B 227 ASP cc_start: 0.8808 (m-30) cc_final: 0.8403 (p0) REVERT: C 34 LYS cc_start: 0.9331 (mmmt) cc_final: 0.9008 (mtpt) REVERT: C 121 LEU cc_start: 0.8889 (mp) cc_final: 0.8598 (pp) REVERT: C 137 ASN cc_start: 0.8974 (t0) cc_final: 0.8630 (t0) REVERT: C 221 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8868 (mm) REVERT: D 142 ASN cc_start: 0.9106 (m-40) cc_final: 0.8197 (p0) REVERT: D 166 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.9171 (m-30) REVERT: E 56 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7844 (p90) REVERT: E 94 ILE cc_start: 0.8968 (tp) cc_final: 0.8611 (pt) REVERT: E 105 ASN cc_start: 0.9149 (t0) cc_final: 0.8811 (t0) REVERT: F 92 VAL cc_start: 0.9238 (t) cc_final: 0.8943 (p) REVERT: F 140 LYS cc_start: 0.7573 (ptpt) cc_final: 0.6662 (tmmt) REVERT: F 142 ASN cc_start: 0.9314 (p0) cc_final: 0.8854 (p0) REVERT: F 172 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7950 (mt-10) REVERT: G 68 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9174 (mm) REVERT: G 131 ARG cc_start: 0.8416 (ppt170) cc_final: 0.8056 (tmt170) REVERT: G 176 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7257 (t80) REVERT: I 893 VAL cc_start: 0.8931 (t) cc_final: 0.8718 (p) REVERT: I 897 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7549 (tp30) outliers start: 48 outliers final: 39 residues processed: 162 average time/residue: 0.1545 time to fit residues: 39.3408 Evaluate side-chains 168 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 147 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 0.0670 chunk 181 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.078605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054224 restraints weight = 56247.442| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.50 r_work: 0.2743 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20955 Z= 0.169 Angle : 0.547 13.060 28544 Z= 0.268 Chirality : 0.040 0.192 3197 Planarity : 0.003 0.041 3523 Dihedral : 13.025 103.526 3277 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.48 % Allowed : 16.66 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2407 helix: 1.77 (0.14), residues: 1452 sheet: -0.13 (0.40), residues: 196 loop : 0.33 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 215 TYR 0.021 0.001 TYR G 110 PHE 0.021 0.001 PHE H 898 TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (20955) covalent geometry : angle 0.54677 / 0.27 (28544) hydrogen bonds : bond 0.03736 / 2.48 ( 1078) hydrogen bonds : angle 3.55821 / 2.56 ( 2933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8511 (p90) cc_final: 0.8201 (t80) REVERT: A 142 ASN cc_start: 0.8174 (m110) cc_final: 0.7765 (m110) REVERT: A 164 HIS cc_start: 0.8862 (t-90) cc_final: 0.8158 (t-90) REVERT: A 198 MET cc_start: 0.7886 (mtm) cc_final: 0.7406 (ptp) REVERT: B 73 LYS cc_start: 0.9093 (tptm) cc_final: 0.8653 (tppt) REVERT: B 137 ASN cc_start: 0.7926 (t0) cc_final: 0.7665 (p0) REVERT: B 220 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: B 227 ASP cc_start: 0.8761 (m-30) cc_final: 0.8407 (p0) REVERT: C 34 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9065 (mtpt) REVERT: C 121 LEU cc_start: 0.8888 (mp) cc_final: 0.8615 (pp) REVERT: C 137 ASN cc_start: 0.9009 (t0) cc_final: 0.8678 (t0) REVERT: C 221 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8922 (mm) REVERT: D 142 ASN cc_start: 0.9138 (m-40) cc_final: 0.8240 (p0) REVERT: D 166 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.9171 (m-30) REVERT: E 56 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7863 (p90) REVERT: E 94 ILE cc_start: 0.9000 (tp) cc_final: 0.8664 (pt) REVERT: E 105 ASN cc_start: 0.9174 (t0) cc_final: 0.8868 (t0) REVERT: F 92 VAL cc_start: 0.9261 (t) cc_final: 0.8979 (p) REVERT: F 140 LYS cc_start: 0.7571 (ptpt) cc_final: 0.6653 (tmmt) REVERT: F 142 ASN cc_start: 0.9303 (p0) cc_final: 0.8841 (p0) REVERT: F 172 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8003 (mt-10) REVERT: G 41 MET cc_start: 0.9375 (tpp) cc_final: 0.9109 (tpp) REVERT: G 68 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9223 (mm) REVERT: G 131 ARG cc_start: 0.8425 (ppt170) cc_final: 0.8068 (tmt170) REVERT: I 897 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7553 (tp30) outliers start: 52 outliers final: 42 residues processed: 170 average time/residue: 0.1458 time to fit residues: 38.7987 Evaluate side-chains 173 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 19 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 173 optimal weight: 0.0010 chunk 218 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055573 restraints weight = 56059.331| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.47 r_work: 0.2777 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20955 Z= 0.104 Angle : 0.523 13.449 28544 Z= 0.256 Chirality : 0.039 0.180 3197 Planarity : 0.003 0.041 3523 Dihedral : 12.925 100.757 3277 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.09 % Allowed : 16.99 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2407 helix: 1.80 (0.14), residues: 1452 sheet: -0.10 (0.40), residues: 196 loop : 0.35 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.024 0.001 TYR G 110 PHE 0.018 0.001 PHE H 898 TRP 0.005 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (20955) covalent geometry : angle 0.52306 / 0.26 (28544) hydrogen bonds : bond 0.03546 / 2.36 ( 1078) hydrogen bonds : angle 3.47162 / 2.49 ( 2933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8488 (p90) cc_final: 0.8211 (t80) REVERT: A 142 ASN cc_start: 0.8191 (m110) cc_final: 0.7798 (m110) REVERT: A 164 HIS cc_start: 0.8870 (t-90) cc_final: 0.8167 (t-90) REVERT: A 198 MET cc_start: 0.8000 (mtm) cc_final: 0.7419 (ptp) REVERT: B 73 LYS cc_start: 0.9093 (tptm) cc_final: 0.8640 (tppt) REVERT: B 137 ASN cc_start: 0.7893 (t0) cc_final: 0.7640 (p0) REVERT: B 227 ASP cc_start: 0.8716 (m-30) cc_final: 0.8449 (p0) REVERT: C 34 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9066 (mtpt) REVERT: C 103 TYR cc_start: 0.8425 (p90) cc_final: 0.8031 (p90) REVERT: C 121 LEU cc_start: 0.8871 (mp) cc_final: 0.8590 (pp) REVERT: C 137 ASN cc_start: 0.8966 (t0) cc_final: 0.8630 (t0) REVERT: C 221 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8934 (mm) REVERT: D 142 ASN cc_start: 0.9134 (m-40) cc_final: 0.8261 (p0) REVERT: D 166 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.9181 (m-30) REVERT: E 56 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7843 (p90) REVERT: E 94 ILE cc_start: 0.9023 (tp) cc_final: 0.8729 (pt) REVERT: E 105 ASN cc_start: 0.9186 (t0) cc_final: 0.8856 (t0) REVERT: F 92 VAL cc_start: 0.9265 (t) cc_final: 0.9002 (p) REVERT: F 140 LYS cc_start: 0.7575 (ptpt) cc_final: 0.6644 (tmmt) REVERT: F 142 ASN cc_start: 0.9299 (p0) cc_final: 0.8836 (p0) REVERT: F 172 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7953 (mt-10) REVERT: G 68 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9229 (mm) REVERT: G 131 ARG cc_start: 0.8442 (ppt170) cc_final: 0.8077 (tmt170) REVERT: I 897 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7594 (tp30) REVERT: J 897 GLU cc_start: 0.8767 (tt0) cc_final: 0.8223 (tm-30) outliers start: 44 outliers final: 34 residues processed: 159 average time/residue: 0.1457 time to fit residues: 36.4044 Evaluate side-chains 161 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 38 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054916 restraints weight = 56258.942| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.46 r_work: 0.2762 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20955 Z= 0.145 Angle : 0.541 14.154 28544 Z= 0.264 Chirality : 0.040 0.241 3197 Planarity : 0.003 0.041 3523 Dihedral : 12.920 99.868 3277 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.09 % Allowed : 16.99 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.18), residues: 2407 helix: 1.82 (0.14), residues: 1451 sheet: -0.10 (0.40), residues: 196 loop : 0.33 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.024 0.001 TYR G 110 PHE 0.018 0.001 PHE H 898 TRP 0.006 0.001 TRP F 267 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (20955) covalent geometry : angle 0.54083 / 0.26 (28544) hydrogen bonds : bond 0.03593 / 2.39 ( 1078) hydrogen bonds : angle 3.50348 / 2.51 ( 2933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.55 seconds wall clock time: 71 minutes 56.26 seconds (4316.26 seconds total)