Starting phenix.real_space_refine on Wed Jun 18 00:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmz_51458/06_2025/9gmz_51458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmz_51458/06_2025/9gmz_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_51458/06_2025/9gmz_51458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmz_51458/06_2025/9gmz_51458.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmz_51458/06_2025/9gmz_51458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmz_51458/06_2025/9gmz_51458.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.60, per 1000 atoms: 0.66 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: 4.77 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 6.87 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: 7.08 Time building geometry restraints manager: 5.71 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: 28163 2.33 - 4.66: 322 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: 2958 0.087 - 0.174: 218 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: 0.010 Normalize map: mean=0, sd=1: 6.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.930 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.520 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.120 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20955 Z= 0.220 Angle : 0.644 11.650 28544 Z= 0.370 Chirality : 0.046 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP C 284 HIS 0.003 0.001 HIS G 30 PHE 0.038 0.001 PHE G 126 TYR 0.034 0.001 TYR G 110 ARG 0.005 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.16020 ( 1078) hydrogen bonds : angle 4.63898 ( 2933) covalent geometry : bond 0.00344 (20955) covalent geometry : angle 0.64412 (28544) *********************** 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 : 2.534 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: 0.8300 (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: 0.7634 (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: 0.3929 time to fit residues: 114.7102 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 : 2.358 ------------------------------------------------------------------------------- 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 201 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN B 197 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS D 242 GLN E 216 ASN E 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.081886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057362 restraints weight = 56069.711| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.62 r_work: 0.2808 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20955 Z= 0.153 Angle : 0.543 9.923 28544 Z= 0.275 Chirality : 0.040 0.217 3197 Planarity : 0.004 0.043 3523 Dihedral : 13.152 115.319 3301 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.43 % Allowed : 14.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.18), residues: 2407 helix: 1.62 (0.14), residues: 1465 sheet: 0.29 (0.40), residues: 196 loop : 0.59 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS C 175 PHE 0.026 0.001 PHE D 319 TYR 0.012 0.001 TYR G 109 ARG 0.004 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 1078) hydrogen bonds : angle 3.77938 ( 2933) covalent geometry : bond 0.00341 (20955) covalent geometry : angle 0.54340 (28544) *********************** 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 200 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8463 (p90) cc_final: 0.8117 (t80) REVERT: A 142 ASN cc_start: 0.8085 (m110) cc_final: 0.7622 (m110) REVERT: A 164 HIS cc_start: 0.8748 (t-90) cc_final: 0.7994 (t-90) REVERT: A 198 MET cc_start: 0.7929 (mtm) cc_final: 0.7437 (ptp) REVERT: A 328 GLN cc_start: 0.8324 (mt0) cc_final: 0.8040 (mp10) REVERT: B 73 LYS cc_start: 0.9063 (tptm) cc_final: 0.8627 (tppt) REVERT: B 137 ASN cc_start: 0.7838 (t0) cc_final: 0.7351 (p0) REVERT: B 220 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: B 227 ASP cc_start: 0.8806 (m-30) cc_final: 0.8370 (p0) REVERT: C 34 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8899 (mtpt) REVERT: C 69 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8471 (tpp80) REVERT: C 121 LEU cc_start: 0.8900 (mp) cc_final: 0.8550 (pp) REVERT: C 137 ASN cc_start: 0.8958 (t0) cc_final: 0.8537 (t0) REVERT: C 221 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8838 (mm) REVERT: C 307 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8908 (tppt) REVERT: D 14 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8184 (mmm160) REVERT: D 24 GLU cc_start: 0.9332 (tp30) cc_final: 0.8942 (tp30) REVERT: E 56 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7817 (p90) REVERT: E 94 ILE cc_start: 0.8968 (tp) cc_final: 0.8652 (pt) REVERT: E 102 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7459 (ttp-110) REVERT: E 103 TYR cc_start: 0.7948 (p90) cc_final: 0.7727 (p90) REVERT: E 105 ASN cc_start: 0.9109 (t0) cc_final: 0.8886 (t0) REVERT: E 262 ASN cc_start: 0.8787 (t0) cc_final: 0.8447 (t0) REVERT: F 119 GLU cc_start: 0.6716 (tp30) cc_final: 0.6477 (pt0) REVERT: F 140 LYS cc_start: 0.7534 (ptpt) cc_final: 0.6586 (tmmt) REVERT: F 142 ASN cc_start: 0.9315 (p0) cc_final: 0.8515 (p0) REVERT: F 172 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7900 (mt-10) REVERT: G 41 MET cc_start: 0.9369 (tpt) cc_final: 0.9093 (tpt) REVERT: G 271 TYR cc_start: 0.7880 (t80) cc_final: 0.7540 (t80) REVERT: H 898 PHE cc_start: 0.7147 (t80) cc_final: 0.6769 (t80) REVERT: I 893 VAL cc_start: 0.8430 (t) cc_final: 0.8147 (p) REVERT: I 897 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7386 (tp30) REVERT: J 895 TYR cc_start: 0.8741 (m-80) cc_final: 0.8458 (m-80) REVERT: M 894 VAL cc_start: 0.9040 (t) cc_final: 0.8826 (t) outliers start: 51 outliers final: 21 residues processed: 187 average time/residue: 0.3610 time to fit residues: 102.9532 Evaluate side-chains 161 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 56 TYR 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 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 221 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 145 SER 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 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 117 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 112 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN D 203 HIS E 216 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.077735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053048 restraints weight = 56402.802| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.55 r_work: 0.2707 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20955 Z= 0.268 Angle : 0.628 9.348 28544 Z= 0.316 Chirality : 0.043 0.151 3197 Planarity : 0.004 0.044 3523 Dihedral : 13.201 113.178 3288 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.19 % Allowed : 14.90 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2407 helix: 1.44 (0.14), residues: 1470 sheet: 0.01 (0.38), residues: 196 loop : 0.36 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 284 HIS 0.005 0.001 HIS C 175 PHE 0.017 0.002 PHE D 23 TYR 0.031 0.002 TYR G 110 ARG 0.016 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1078) hydrogen bonds : angle 3.92664 ( 2933) covalent geometry : bond 0.00617 (20955) covalent geometry : angle 0.62802 (28544) *********************** 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 196 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8484 (p90) cc_final: 0.8100 (t80) REVERT: A 142 ASN cc_start: 0.8159 (m110) cc_final: 0.7689 (m110) REVERT: A 164 HIS cc_start: 0.8814 (t-90) cc_final: 0.8111 (t-90) REVERT: A 198 MET cc_start: 0.7867 (mtm) cc_final: 0.7362 (ptp) REVERT: A 328 GLN cc_start: 0.8292 (mt0) cc_final: 0.8019 (mp10) REVERT: B 137 ASN cc_start: 0.7828 (t0) cc_final: 0.7427 (p0) REVERT: B 220 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7669 (tp40) REVERT: B 227 ASP cc_start: 0.8798 (m-30) cc_final: 0.8434 (p0) REVERT: C 34 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9091 (mtpt) REVERT: C 56 TYR cc_start: 0.8809 (m-80) cc_final: 0.8424 (m-80) REVERT: C 69 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8477 (tpp80) REVERT: C 121 LEU cc_start: 0.8887 (mp) cc_final: 0.8609 (pp) REVERT: C 137 ASN cc_start: 0.8971 (t0) cc_final: 0.8658 (t0) REVERT: C 221 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8963 (mm) REVERT: D 41 MET cc_start: 0.9065 (mmm) cc_final: 0.8854 (mmm) REVERT: D 142 ASN cc_start: 0.9087 (m-40) cc_final: 0.8140 (p0) REVERT: D 166 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.9165 (m-30) REVERT: E 56 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8050 (p90) REVERT: F 14 ARG cc_start: 0.9026 (mmp80) cc_final: 0.8651 (mtt90) REVERT: F 92 VAL cc_start: 0.9277 (t) cc_final: 0.8983 (p) REVERT: F 94 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8860 (pt) REVERT: F 140 LYS cc_start: 0.7586 (ptpt) cc_final: 0.6660 (tmmt) REVERT: F 142 ASN cc_start: 0.9317 (p0) cc_final: 0.8628 (p0) REVERT: F 172 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8066 (mt-10) REVERT: G 68 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9244 (mm) REVERT: G 131 ARG cc_start: 0.8438 (ppt170) cc_final: 0.8102 (tmt170) REVERT: G 176 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7388 (t80) REVERT: G 271 TYR cc_start: 0.7912 (t80) cc_final: 0.7685 (t80) REVERT: H 898 PHE cc_start: 0.7526 (t80) cc_final: 0.7314 (t80) REVERT: I 893 VAL cc_start: 0.8836 (t) cc_final: 0.8625 (p) REVERT: I 897 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7490 (tp30) outliers start: 67 outliers final: 31 residues processed: 185 average time/residue: 0.3233 time to fit residues: 93.4169 Evaluate side-chains 160 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 91 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 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 77 LEU 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 166 ASP 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 152 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 94 ILE 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 L residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN G 25 ASN ** G 197 ASN ** 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 = 0.3468 r_free = 0.3468 target = 0.080136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055593 restraints weight = 56310.278| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.60 r_work: 0.2793 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2113 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= 0.116 Angle : 0.503 9.972 28544 Z= 0.251 Chirality : 0.039 0.199 3197 Planarity : 0.004 0.053 3523 Dihedral : 12.888 108.449 3282 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.38 % Allowed : 15.23 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.18), residues: 2407 helix: 1.66 (0.14), residues: 1456 sheet: -0.05 (0.39), residues: 196 loop : 0.48 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.014 0.001 PHE F 138 TYR 0.030 0.001 TYR G 110 ARG 0.003 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1078) hydrogen bonds : angle 3.55820 ( 2933) covalent geometry : bond 0.00263 (20955) covalent geometry : angle 0.50251 (28544) *********************** 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 194 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8465 (p90) cc_final: 0.8142 (t80) REVERT: A 142 ASN cc_start: 0.8126 (m110) cc_final: 0.7698 (m110) REVERT: A 164 HIS cc_start: 0.8842 (t-90) cc_final: 0.8138 (t-90) REVERT: A 198 MET cc_start: 0.7852 (mtm) cc_final: 0.7350 (ptp) REVERT: B 73 LYS cc_start: 0.9047 (tptm) cc_final: 0.8600 (tppt) REVERT: B 137 ASN cc_start: 0.7848 (t0) cc_final: 0.7511 (p0) REVERT: B 220 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7794 (tp40) REVERT: B 227 ASP cc_start: 0.8774 (m-30) cc_final: 0.8440 (p0) REVERT: C 34 LYS cc_start: 0.9333 (mmmt) cc_final: 0.9008 (mtpt) REVERT: C 69 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (tpp80) REVERT: C 103 TYR cc_start: 0.8432 (p90) cc_final: 0.8029 (p90) REVERT: C 121 LEU cc_start: 0.8875 (mp) cc_final: 0.8578 (pp) REVERT: C 137 ASN cc_start: 0.9023 (t0) cc_final: 0.8641 (t0) REVERT: D 142 ASN cc_start: 0.9050 (m-40) cc_final: 0.8123 (p0) REVERT: E 56 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7909 (p90) REVERT: E 94 ILE cc_start: 0.8988 (tp) cc_final: 0.8650 (pt) REVERT: F 92 VAL cc_start: 0.9280 (t) cc_final: 0.9020 (p) REVERT: F 140 LYS cc_start: 0.7577 (ptpt) cc_final: 0.6650 (tmmt) REVERT: F 142 ASN cc_start: 0.9320 (p0) cc_final: 0.8855 (p0) REVERT: F 172 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7912 (mt-10) REVERT: G 131 ARG cc_start: 0.8443 (ppt170) cc_final: 0.8113 (tmt170) REVERT: I 893 VAL cc_start: 0.8906 (t) cc_final: 0.8665 (p) REVERT: I 897 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7587 (tp30) outliers start: 50 outliers final: 27 residues processed: 183 average time/residue: 0.3284 time to fit residues: 94.3861 Evaluate side-chains 157 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN 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 198 MET 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 103 TYR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN 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 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 J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 215 optimal weight: 0.0000 chunk 3 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3463 r_free = 0.3463 target = 0.079929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055388 restraints weight = 56917.425| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.62 r_work: 0.2784 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2257 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= 0.124 Angle : 0.507 9.686 28544 Z= 0.250 Chirality : 0.039 0.273 3197 Planarity : 0.003 0.051 3523 Dihedral : 12.773 104.670 3282 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.76 % Allowed : 16.09 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.18), residues: 2407 helix: 1.80 (0.14), residues: 1451 sheet: 0.00 (0.39), residues: 196 loop : 0.44 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.013 0.001 PHE F 138 TYR 0.034 0.001 TYR G 110 ARG 0.003 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 1078) hydrogen bonds : angle 3.48284 ( 2933) covalent geometry : bond 0.00281 (20955) covalent geometry : angle 0.50651 (28544) *********************** 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 196 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8496 (p90) cc_final: 0.8163 (t80) REVERT: A 142 ASN cc_start: 0.8130 (m110) cc_final: 0.7716 (m110) REVERT: A 164 HIS cc_start: 0.8860 (t-90) cc_final: 0.8160 (t-90) REVERT: A 198 MET cc_start: 0.7873 (mtm) cc_final: 0.7367 (ptp) REVERT: A 221 LEU cc_start: 0.3558 (OUTLIER) cc_final: 0.3299 (mt) REVERT: B 73 LYS cc_start: 0.9048 (tptm) cc_final: 0.8596 (tppt) REVERT: B 142 ASN cc_start: 0.8408 (t0) cc_final: 0.8123 (t0) REVERT: B 172 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.9021 (mt-10) REVERT: B 220 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7612 (tp40) REVERT: B 227 ASP cc_start: 0.8780 (m-30) cc_final: 0.8457 (p0) REVERT: C 34 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9033 (mtpt) REVERT: C 69 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8372 (tpp80) REVERT: C 103 TYR cc_start: 0.8427 (p90) cc_final: 0.8055 (p90) REVERT: C 121 LEU cc_start: 0.8884 (mp) cc_final: 0.8577 (pp) REVERT: C 137 ASN cc_start: 0.9013 (t0) cc_final: 0.8678 (t0) REVERT: C 221 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 142 ASN cc_start: 0.9088 (m-40) cc_final: 0.8190 (p0) REVERT: E 56 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7910 (p90) REVERT: E 94 ILE cc_start: 0.8977 (tp) cc_final: 0.8649 (pt) REVERT: E 105 ASN cc_start: 0.9107 (t0) cc_final: 0.8864 (t0) REVERT: F 92 VAL cc_start: 0.9278 (t) cc_final: 0.9018 (p) REVERT: F 140 LYS cc_start: 0.7569 (ptpt) cc_final: 0.6637 (tmmt) REVERT: F 142 ASN cc_start: 0.9298 (p0) cc_final: 0.8831 (p0) REVERT: F 172 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7911 (mt-10) REVERT: G 131 ARG cc_start: 0.8467 (ppt170) cc_final: 0.8175 (tmt170) REVERT: G 176 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7190 (t80) REVERT: G 178 LYS cc_start: 0.6990 (mptt) cc_final: 0.6535 (mmtm) REVERT: I 897 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7629 (tp30) outliers start: 58 outliers final: 33 residues processed: 184 average time/residue: 0.3997 time to fit residues: 113.3262 Evaluate side-chains 165 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 221 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 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 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 234 CYS Chi-restraints excluded: chain D residue 252 GLN 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 9 LEU 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 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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 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 140 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.0000 chunk 177 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN C 124 HIS ** 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 = 0.3475 r_free = 0.3475 target = 0.080611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056460 restraints weight = 56305.454| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.58 r_work: 0.2812 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20955 Z= 0.102 Angle : 0.494 12.266 28544 Z= 0.243 Chirality : 0.039 0.195 3197 Planarity : 0.003 0.047 3523 Dihedral : 12.650 100.332 3282 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.57 % Allowed : 16.42 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2407 helix: 1.87 (0.14), residues: 1451 sheet: 0.03 (0.39), residues: 196 loop : 0.43 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.013 0.001 PHE F 138 TYR 0.031 0.001 TYR G 110 ARG 0.005 0.000 ARG F 112 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 1078) hydrogen bonds : angle 3.39608 ( 2933) covalent geometry : bond 0.00228 (20955) covalent geometry : angle 0.49402 (28544) *********************** 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 190 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8464 (p90) cc_final: 0.8198 (t80) REVERT: A 142 ASN cc_start: 0.8181 (m110) cc_final: 0.7789 (m110) REVERT: A 164 HIS cc_start: 0.8876 (t-90) cc_final: 0.8133 (t-90) REVERT: A 198 MET cc_start: 0.7900 (mtm) cc_final: 0.7443 (ptp) REVERT: A 221 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.3277 (mt) REVERT: B 73 LYS cc_start: 0.9044 (tptm) cc_final: 0.8585 (tppt) REVERT: B 137 ASN cc_start: 0.7758 (t0) cc_final: 0.7197 (p0) REVERT: B 142 ASN cc_start: 0.8400 (t0) cc_final: 0.8114 (t0) REVERT: B 172 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8956 (mt-10) REVERT: B 220 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: B 227 ASP cc_start: 0.8736 (m-30) cc_final: 0.8434 (p0) REVERT: C 34 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9028 (mtpt) REVERT: C 69 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8317 (tpp80) REVERT: C 103 TYR cc_start: 0.8354 (p90) cc_final: 0.8016 (p90) REVERT: C 121 LEU cc_start: 0.8878 (mp) cc_final: 0.8582 (pp) REVERT: C 137 ASN cc_start: 0.8985 (t0) cc_final: 0.8634 (t0) REVERT: C 198 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: C 221 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8826 (mm) REVERT: D 142 ASN cc_start: 0.9064 (m-40) cc_final: 0.8210 (p0) REVERT: E 56 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7884 (p90) REVERT: E 94 ILE cc_start: 0.8990 (tp) cc_final: 0.8700 (pt) REVERT: F 92 VAL cc_start: 0.9277 (t) cc_final: 0.9035 (p) REVERT: F 140 LYS cc_start: 0.7563 (ptpt) cc_final: 0.6489 (tmmt) REVERT: F 142 ASN cc_start: 0.9299 (p0) cc_final: 0.8533 (p0) REVERT: F 172 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7821 (mt-10) REVERT: G 41 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8975 (tpp) REVERT: G 103 TYR cc_start: 0.8015 (p90) cc_final: 0.7680 (p90) REVERT: G 131 ARG cc_start: 0.8497 (ppt170) cc_final: 0.8224 (tmt170) REVERT: G 176 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7185 (t80) REVERT: G 178 LYS cc_start: 0.7019 (mptt) cc_final: 0.6553 (mmtm) REVERT: I 897 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7630 (tp30) outliers start: 54 outliers final: 31 residues processed: 180 average time/residue: 0.4284 time to fit residues: 120.1833 Evaluate side-chains 167 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 2.664 ------------------------------------------------------------------------------- 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 221 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 157 GLU Chi-restraints excluded: chain B residue 172 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 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 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 252 GLN 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 9 LEU 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 G residue 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 33 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3481 r_free = 0.3481 target = 0.080722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057169 restraints weight = 57301.846| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.32 r_work: 0.2815 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20955 Z= 0.116 Angle : 0.502 11.754 28544 Z= 0.245 Chirality : 0.039 0.181 3197 Planarity : 0.003 0.054 3523 Dihedral : 12.564 95.616 3280 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.52 % Allowed : 16.71 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2407 helix: 1.92 (0.14), residues: 1451 sheet: 0.03 (0.39), residues: 196 loop : 0.44 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.030 0.001 TYR G 110 ARG 0.002 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 1078) hydrogen bonds : angle 3.36873 ( 2933) covalent geometry : bond 0.00264 (20955) covalent geometry : angle 0.50154 (28544) *********************** 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 182 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8351 (m110) cc_final: 0.7978 (m110) REVERT: A 164 HIS cc_start: 0.8864 (t-90) cc_final: 0.8100 (t-90) REVERT: A 198 MET cc_start: 0.8077 (mtm) cc_final: 0.7521 (ptp) REVERT: A 221 LEU cc_start: 0.3630 (OUTLIER) cc_final: 0.3336 (mt) REVERT: B 73 LYS cc_start: 0.9137 (tptm) cc_final: 0.8719 (tppt) REVERT: B 172 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8977 (mt-10) REVERT: B 220 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7808 (tp40) REVERT: B 227 ASP cc_start: 0.8621 (m-30) cc_final: 0.8326 (p0) REVERT: C 34 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9149 (mtpt) REVERT: C 56 TYR cc_start: 0.8716 (m-80) cc_final: 0.8353 (m-80) REVERT: C 103 TYR cc_start: 0.8415 (p90) cc_final: 0.8101 (p90) REVERT: C 121 LEU cc_start: 0.8823 (mp) cc_final: 0.8609 (pp) REVERT: C 137 ASN cc_start: 0.8900 (t0) cc_final: 0.8582 (t0) REVERT: C 198 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: C 221 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9002 (mm) REVERT: C 286 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8468 (tptp) REVERT: D 142 ASN cc_start: 0.9117 (m-40) cc_final: 0.8348 (p0) REVERT: E 56 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7991 (p90) REVERT: E 94 ILE cc_start: 0.9071 (tp) cc_final: 0.8840 (pt) REVERT: E 105 ASN cc_start: 0.9050 (t0) cc_final: 0.8784 (t0) REVERT: F 140 LYS cc_start: 0.7536 (ptpt) cc_final: 0.6480 (tmmt) REVERT: F 142 ASN cc_start: 0.9258 (p0) cc_final: 0.8492 (p0) REVERT: F 172 GLU cc_start: 0.8615 (mm-30) cc_final: 0.7929 (mt-10) REVERT: G 41 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8855 (tpp) REVERT: G 131 ARG cc_start: 0.8498 (ppt170) cc_final: 0.8237 (tmt170) REVERT: G 176 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7216 (t80) REVERT: I 897 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7634 (tp30) outliers start: 53 outliers final: 36 residues processed: 172 average time/residue: 0.3677 time to fit residues: 99.1961 Evaluate side-chains 165 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 2.828 ------------------------------------------------------------------------------- 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 221 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 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 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 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 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 C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 185 LEU 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 76 GLU 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 9 LEU 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 G residue 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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 L residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 59 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 64 optimal weight: 0.3980 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3476 r_free = 0.3476 target = 0.080486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.057082 restraints weight = 57436.378| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.31 r_work: 0.2813 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20955 Z= 0.118 Angle : 0.506 13.958 28544 Z= 0.247 Chirality : 0.039 0.310 3197 Planarity : 0.003 0.056 3523 Dihedral : 12.497 90.764 3276 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.33 % Allowed : 17.04 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2407 helix: 1.93 (0.14), residues: 1451 sheet: 0.01 (0.39), residues: 196 loop : 0.44 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.032 0.001 TYR G 110 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 1078) hydrogen bonds : angle 3.36877 ( 2933) covalent geometry : bond 0.00269 (20955) covalent geometry : angle 0.50601 (28544) *********************** 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 173 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8371 (m110) cc_final: 0.8007 (m110) REVERT: A 164 HIS cc_start: 0.8868 (t-90) cc_final: 0.8105 (t-90) REVERT: A 198 MET cc_start: 0.8077 (mtm) cc_final: 0.7548 (ptp) REVERT: A 221 LEU cc_start: 0.3616 (OUTLIER) cc_final: 0.3308 (mt) REVERT: B 73 LYS cc_start: 0.9134 (tptm) cc_final: 0.8724 (tppt) REVERT: B 137 ASN cc_start: 0.7626 (t0) cc_final: 0.7045 (p0) REVERT: B 172 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8977 (mt-10) REVERT: B 220 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7797 (tp40) REVERT: B 227 ASP cc_start: 0.8603 (m-30) cc_final: 0.8320 (p0) REVERT: C 34 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9143 (mtpt) REVERT: C 56 TYR cc_start: 0.8715 (m-80) cc_final: 0.8310 (m-80) REVERT: C 103 TYR cc_start: 0.8423 (p90) cc_final: 0.8112 (p90) REVERT: C 121 LEU cc_start: 0.8809 (mp) cc_final: 0.8591 (pp) REVERT: C 137 ASN cc_start: 0.8911 (t0) cc_final: 0.8594 (t0) REVERT: C 198 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8359 (mtp) REVERT: C 221 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8993 (mm) REVERT: C 286 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.8466 (tptp) REVERT: D 142 ASN cc_start: 0.9130 (m-40) cc_final: 0.8368 (p0) REVERT: E 56 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7989 (p90) REVERT: E 94 ILE cc_start: 0.9037 (tp) cc_final: 0.8807 (pt) REVERT: E 105 ASN cc_start: 0.9062 (t0) cc_final: 0.8775 (t0) REVERT: E 121 LEU cc_start: 0.7509 (tt) cc_final: 0.6871 (pt) REVERT: F 9 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9047 (mm) REVERT: F 140 LYS cc_start: 0.7492 (ptpt) cc_final: 0.6409 (tmmt) REVERT: F 142 ASN cc_start: 0.9267 (p0) cc_final: 0.8548 (p0) REVERT: F 172 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7928 (mt-10) REVERT: G 41 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9017 (tpp) REVERT: G 95 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: G 131 ARG cc_start: 0.8490 (ppt170) cc_final: 0.8230 (tmt170) REVERT: I 897 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7629 (tp30) outliers start: 49 outliers final: 35 residues processed: 163 average time/residue: 0.4246 time to fit residues: 111.5453 Evaluate side-chains 166 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 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 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 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 148 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 C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 221 LEU 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 76 GLU 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 9 LEU 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 G residue 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 160 optimal weight: 0.0980 chunk 233 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 110 optimal weight: 0.0570 chunk 126 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3497 r_free = 0.3497 target = 0.081552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058118 restraints weight = 57301.555| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.34 r_work: 0.2838 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2634 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= 0.096 Angle : 0.496 13.789 28544 Z= 0.241 Chirality : 0.039 0.302 3197 Planarity : 0.003 0.055 3523 Dihedral : 12.365 82.038 3276 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.00 % Allowed : 17.42 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2407 helix: 1.97 (0.14), residues: 1451 sheet: 0.06 (0.45), residues: 131 loop : 0.30 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.013 0.001 PHE F 138 TYR 0.027 0.001 TYR G 110 ARG 0.003 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 1078) hydrogen bonds : angle 3.30338 ( 2933) covalent geometry : bond 0.00213 (20955) covalent geometry : angle 0.49601 (28544) *********************** 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 175 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8379 (m110) cc_final: 0.8037 (m110) REVERT: A 164 HIS cc_start: 0.8882 (t-90) cc_final: 0.8115 (t-90) REVERT: A 198 MET cc_start: 0.8087 (mtm) cc_final: 0.7570 (ptp) REVERT: A 221 LEU cc_start: 0.3718 (OUTLIER) cc_final: 0.3401 (mt) REVERT: B 73 LYS cc_start: 0.9122 (tptm) cc_final: 0.8714 (tppt) REVERT: B 227 ASP cc_start: 0.8586 (m-30) cc_final: 0.8346 (p0) REVERT: C 34 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9155 (mtpt) REVERT: C 103 TYR cc_start: 0.8412 (p90) cc_final: 0.8146 (p90) REVERT: C 137 ASN cc_start: 0.8921 (t0) cc_final: 0.8589 (t0) REVERT: C 198 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8416 (mtp) REVERT: C 221 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8989 (mm) REVERT: C 286 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8463 (tptp) REVERT: D 24 GLU cc_start: 0.9200 (tp30) cc_final: 0.8812 (tp30) REVERT: D 142 ASN cc_start: 0.9136 (m-40) cc_final: 0.8417 (p0) REVERT: E 56 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7996 (p90) REVERT: E 105 ASN cc_start: 0.9030 (t0) cc_final: 0.8728 (t0) REVERT: E 121 LEU cc_start: 0.7228 (tt) cc_final: 0.6775 (pt) REVERT: F 25 ASN cc_start: 0.9420 (m-40) cc_final: 0.9122 (t0) REVERT: F 140 LYS cc_start: 0.7513 (ptpt) cc_final: 0.6378 (tmmt) REVERT: F 142 ASN cc_start: 0.9201 (p0) cc_final: 0.8416 (p0) REVERT: G 41 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9019 (tpp) REVERT: G 95 GLU cc_start: 0.8547 (tt0) cc_final: 0.8087 (tm-30) REVERT: G 131 ARG cc_start: 0.8507 (ppt170) cc_final: 0.8260 (tmt170) REVERT: I 897 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7651 (tp30) outliers start: 42 outliers final: 29 residues processed: 167 average time/residue: 0.4581 time to fit residues: 123.4809 Evaluate side-chains 158 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 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 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 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 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 C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 76 GLU 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 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 G residue 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 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 = 0.3471 r_free = 0.3471 target = 0.080247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056795 restraints weight = 57507.723| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.31 r_work: 0.2806 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20955 Z= 0.137 Angle : 0.528 14.977 28544 Z= 0.256 Chirality : 0.040 0.304 3197 Planarity : 0.003 0.056 3523 Dihedral : 12.370 77.443 3276 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.00 % Allowed : 17.42 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2407 helix: 1.80 (0.14), residues: 1486 sheet: 0.02 (0.40), residues: 196 loop : 0.25 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 284 HIS 0.005 0.001 HIS A 124 PHE 0.012 0.001 PHE F 138 TYR 0.029 0.001 TYR G 110 ARG 0.003 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 1078) hydrogen bonds : angle 3.37877 ( 2933) covalent geometry : bond 0.00318 (20955) covalent geometry : angle 0.52751 (28544) ********************** 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 168 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8379 (m110) cc_final: 0.8031 (m110) REVERT: A 164 HIS cc_start: 0.8882 (t-90) cc_final: 0.8104 (t-90) REVERT: A 198 MET cc_start: 0.8065 (mtm) cc_final: 0.7535 (ptp) REVERT: A 221 LEU cc_start: 0.3687 (OUTLIER) cc_final: 0.3379 (mt) REVERT: A 283 ASP cc_start: 0.8184 (m-30) cc_final: 0.7882 (t0) REVERT: B 73 LYS cc_start: 0.9140 (tptm) cc_final: 0.8720 (tppt) REVERT: B 220 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8050 (tp40) REVERT: B 227 ASP cc_start: 0.8621 (m-30) cc_final: 0.8328 (p0) REVERT: C 34 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9155 (mtpt) REVERT: C 103 TYR cc_start: 0.8441 (p90) cc_final: 0.8131 (p90) REVERT: C 137 ASN cc_start: 0.8945 (t0) cc_final: 0.8634 (t0) REVERT: C 198 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: C 221 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 105 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.9121 (t0) REVERT: D 142 ASN cc_start: 0.9147 (m-40) cc_final: 0.8424 (p0) REVERT: E 56 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8000 (p90) REVERT: E 105 ASN cc_start: 0.9062 (t0) cc_final: 0.8750 (t0) REVERT: E 121 LEU cc_start: 0.7279 (tt) cc_final: 0.6801 (pt) REVERT: F 25 ASN cc_start: 0.9436 (m-40) cc_final: 0.9153 (t0) REVERT: F 140 LYS cc_start: 0.7482 (ptpt) cc_final: 0.6336 (tmmt) REVERT: F 142 ASN cc_start: 0.9223 (p0) cc_final: 0.8456 (p0) REVERT: F 172 GLU cc_start: 0.8646 (mm-30) cc_final: 0.7952 (mt-10) REVERT: G 41 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8870 (tpp) REVERT: G 131 ARG cc_start: 0.8506 (ppt170) cc_final: 0.8249 (tmt170) REVERT: I 897 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7656 (tp30) outliers start: 42 outliers final: 29 residues processed: 161 average time/residue: 0.5221 time to fit residues: 134.2413 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 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 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 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 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 105 ASN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 76 GLU 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 167 VAL 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 41 MET Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 122 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 111 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 0.0040 chunk 136 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3484 r_free = 0.3484 target = 0.080479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056586 restraints weight = 56138.413| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.46 r_work: 0.2802 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20955 Z= 0.101 Angle : 0.511 14.671 28544 Z= 0.247 Chirality : 0.039 0.294 3197 Planarity : 0.003 0.055 3523 Dihedral : 12.302 75.024 3276 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.90 % Allowed : 17.56 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2407 helix: 1.97 (0.14), residues: 1452 sheet: 0.09 (0.46), residues: 131 loop : 0.29 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 106 HIS 0.004 0.001 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.016 0.001 TYR A 183 ARG 0.007 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 1078) hydrogen bonds : angle 3.31791 ( 2933) covalent geometry : bond 0.00226 (20955) covalent geometry : angle 0.51067 (28544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10568.69 seconds wall clock time: 192 minutes 50.05 seconds (11570.05 seconds total)