Starting phenix.real_space_refine on Tue May 20 22:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmz_51458/05_2025/9gmz_51458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmz_51458/05_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_51458/05_2025/9gmz_51458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmz_51458/05_2025/9gmz_51458.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmz_51458/05_2025/9gmz_51458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmz_51458/05_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-5687/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: 12.66, per 1000 atoms: 0.62 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: 4.52 Conformation dependent library (CDL) restraints added in 2.3 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: 5.94 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: 5.95 Time building geometry restraints manager: 5.33 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: 0.000 Normalize map: mean=0, sd=1: 5.530 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.220 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.750 ------------------------------------------------------------------------------- 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 : 2.363 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: 0.3697 time to fit residues: 107.4642 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 : 2.132 ------------------------------------------------------------------------------- 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: 0.8980 chunk 113 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 G 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058518 restraints weight = 56144.330| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.61 r_work: 0.2823 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20955 Z= 0.140 Angle : 0.534 9.801 28544 Z= 0.271 Chirality : 0.040 0.220 3197 Planarity : 0.004 0.042 3523 Dihedral : 13.156 113.696 3301 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 14.71 % 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: 0.31 (0.40), residues: 196 loop : 0.57 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.026 0.001 PHE D 319 TYR 0.012 0.001 TYR G 109 ARG 0.005 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1078) hydrogen bonds : angle 3.80126 ( 2933) covalent geometry : bond 0.00316 (20955) covalent geometry : angle 0.53437 (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 198 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8472 (p90) cc_final: 0.8119 (t80) REVERT: A 142 ASN cc_start: 0.8085 (m110) cc_final: 0.7616 (m110) REVERT: A 164 HIS cc_start: 0.8742 (t-90) cc_final: 0.7988 (t-90) REVERT: A 198 MET cc_start: 0.7956 (mtm) cc_final: 0.7463 (ptp) REVERT: A 328 GLN cc_start: 0.8323 (mt0) cc_final: 0.8038 (mp10) REVERT: B 73 LYS cc_start: 0.9061 (tptm) cc_final: 0.8627 (tppt) REVERT: B 137 ASN cc_start: 0.7819 (t0) cc_final: 0.7328 (p0) REVERT: B 220 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: B 227 ASP cc_start: 0.8801 (m-30) cc_final: 0.8362 (p0) REVERT: C 34 LYS cc_start: 0.9326 (mmmt) cc_final: 0.8887 (mtpt) REVERT: C 69 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8457 (tpp80) REVERT: C 121 LEU cc_start: 0.8901 (mp) cc_final: 0.8553 (pp) REVERT: C 137 ASN cc_start: 0.8946 (t0) cc_final: 0.8523 (t0) REVERT: C 221 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 307 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8892 (tppt) REVERT: D 24 GLU cc_start: 0.9326 (tp30) cc_final: 0.8994 (tp30) REVERT: E 56 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7742 (p90) REVERT: E 94 ILE cc_start: 0.8980 (tp) cc_final: 0.8682 (pt) REVERT: E 102 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7441 (ttp-110) REVERT: E 103 TYR cc_start: 0.7971 (p90) cc_final: 0.7751 (p90) REVERT: E 105 ASN cc_start: 0.9091 (t0) cc_final: 0.8850 (t0) REVERT: E 262 ASN cc_start: 0.8787 (t0) cc_final: 0.8429 (t0) REVERT: F 119 GLU cc_start: 0.6715 (tp30) cc_final: 0.6475 (pt0) REVERT: F 140 LYS cc_start: 0.7526 (ptpt) cc_final: 0.6564 (tmmt) REVERT: F 142 ASN cc_start: 0.9298 (p0) cc_final: 0.8504 (p0) REVERT: F 172 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7833 (mt-10) REVERT: G 41 MET cc_start: 0.9367 (tpt) cc_final: 0.9095 (tpt) REVERT: G 271 TYR cc_start: 0.7855 (t80) cc_final: 0.7511 (t80) REVERT: H 898 PHE cc_start: 0.7080 (t80) cc_final: 0.6652 (t80) REVERT: I 893 VAL cc_start: 0.8355 (t) cc_final: 0.8067 (p) REVERT: I 897 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7362 (tp30) outliers start: 48 outliers final: 20 residues processed: 185 average time/residue: 0.3388 time to fit residues: 96.0792 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 210 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058290 restraints weight = 55569.442| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.61 r_work: 0.2832 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1406 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= 0.107 Angle : 0.487 8.141 28544 Z= 0.245 Chirality : 0.039 0.138 3197 Planarity : 0.004 0.043 3523 Dihedral : 12.899 111.741 3288 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 15.14 % Favored : 82.44 % 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: 1.80 (0.18), residues: 2407 helix: 1.70 (0.14), residues: 1465 sheet: 0.24 (0.40), residues: 196 loop : 0.64 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.014 0.001 PHE F 138 TYR 0.028 0.001 TYR G 110 ARG 0.004 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1078) hydrogen bonds : angle 3.53754 ( 2933) covalent geometry : bond 0.00237 (20955) covalent geometry : angle 0.48743 (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 203 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8435 (p90) cc_final: 0.8132 (t80) REVERT: A 142 ASN cc_start: 0.8135 (m110) cc_final: 0.7670 (m110) REVERT: A 164 HIS cc_start: 0.8791 (t-90) cc_final: 0.8089 (t-90) REVERT: A 198 MET cc_start: 0.7939 (mtm) cc_final: 0.7446 (ptp) REVERT: A 267 TRP cc_start: 0.9039 (p-90) cc_final: 0.8572 (p-90) REVERT: A 328 GLN cc_start: 0.8348 (mt0) cc_final: 0.8075 (mp10) REVERT: B 73 LYS cc_start: 0.9037 (tptm) cc_final: 0.8612 (tppt) REVERT: B 137 ASN cc_start: 0.7807 (t0) cc_final: 0.7431 (p0) REVERT: B 227 ASP cc_start: 0.8794 (m-30) cc_final: 0.8331 (p0) REVERT: C 34 LYS cc_start: 0.9330 (mmmt) cc_final: 0.8887 (mtpt) REVERT: C 121 LEU cc_start: 0.8872 (mp) cc_final: 0.8533 (pp) REVERT: C 137 ASN cc_start: 0.8949 (t0) cc_final: 0.8564 (t0) REVERT: D 14 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8431 (mmm160) REVERT: D 24 GLU cc_start: 0.9315 (tp30) cc_final: 0.8976 (tp30) REVERT: D 41 MET cc_start: 0.8995 (mmm) cc_final: 0.8760 (mmm) REVERT: D 142 ASN cc_start: 0.9112 (m-40) cc_final: 0.8205 (p0) REVERT: E 56 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7772 (p90) REVERT: E 94 ILE cc_start: 0.8994 (tp) cc_final: 0.8713 (pt) REVERT: E 102 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7508 (ttp-110) REVERT: E 105 ASN cc_start: 0.9095 (t0) cc_final: 0.8868 (t0) REVERT: E 210 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8612 (mp0) REVERT: E 262 ASN cc_start: 0.8799 (t0) cc_final: 0.8448 (t0) REVERT: F 92 VAL cc_start: 0.9309 (t) cc_final: 0.9056 (p) REVERT: F 119 GLU cc_start: 0.6854 (tp30) cc_final: 0.6631 (pt0) REVERT: F 140 LYS cc_start: 0.7506 (ptpt) cc_final: 0.6535 (tmmt) REVERT: F 142 ASN cc_start: 0.9291 (p0) cc_final: 0.8487 (p0) REVERT: F 172 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7827 (mt-10) REVERT: G 41 MET cc_start: 0.9363 (tpt) cc_final: 0.9085 (tpt) REVERT: G 271 TYR cc_start: 0.7838 (t80) cc_final: 0.7531 (t80) REVERT: H 898 PHE cc_start: 0.7169 (t80) cc_final: 0.6803 (t80) REVERT: I 893 VAL cc_start: 0.8459 (t) cc_final: 0.8216 (p) REVERT: I 897 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7384 (tp30) REVERT: K 895 TYR cc_start: 0.8886 (m-80) cc_final: 0.8597 (m-80) REVERT: L 894 VAL cc_start: 0.8881 (p) cc_final: 0.8672 (p) outliers start: 51 outliers final: 23 residues processed: 191 average time/residue: 0.3267 time to fit residues: 96.7333 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 148 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 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- 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 D 203 HIS E 216 ASN G 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.080414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055989 restraints weight = 56549.491| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.61 r_work: 0.2801 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20955 Z= 0.155 Angle : 0.522 10.179 28544 Z= 0.261 Chirality : 0.040 0.207 3197 Planarity : 0.004 0.039 3523 Dihedral : 12.843 109.641 3280 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.33 % Allowed : 15.42 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.18), residues: 2407 helix: 1.84 (0.14), residues: 1450 sheet: 0.17 (0.39), residues: 196 loop : 0.48 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.014 0.001 PHE F 138 TYR 0.026 0.001 TYR G 110 ARG 0.010 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1078) hydrogen bonds : angle 3.56258 ( 2933) covalent geometry : bond 0.00354 (20955) covalent geometry : angle 0.52173 (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 185 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8449 (p90) cc_final: 0.8158 (t80) REVERT: A 142 ASN cc_start: 0.8134 (m110) cc_final: 0.7679 (m110) REVERT: A 164 HIS cc_start: 0.8802 (t-90) cc_final: 0.8074 (t-90) REVERT: A 198 MET cc_start: 0.7945 (mtm) cc_final: 0.7430 (ptp) REVERT: A 328 GLN cc_start: 0.8313 (mt0) cc_final: 0.8068 (mp10) REVERT: B 73 LYS cc_start: 0.9053 (tptm) cc_final: 0.8611 (tppt) REVERT: B 137 ASN cc_start: 0.7800 (t0) cc_final: 0.7489 (p0) REVERT: B 227 ASP cc_start: 0.8800 (m-30) cc_final: 0.8351 (p0) REVERT: C 34 LYS cc_start: 0.9341 (mmmt) cc_final: 0.9006 (mtpt) REVERT: C 121 LEU cc_start: 0.8877 (mp) cc_final: 0.8566 (pp) REVERT: C 137 ASN cc_start: 0.8997 (t0) cc_final: 0.8607 (p0) REVERT: C 221 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 24 GLU cc_start: 0.9355 (tp30) cc_final: 0.8953 (tp30) REVERT: D 41 MET cc_start: 0.8991 (mmm) cc_final: 0.8754 (mmm) REVERT: D 142 ASN cc_start: 0.9105 (m-40) cc_final: 0.8184 (p0) REVERT: D 291 ASP cc_start: 0.9404 (OUTLIER) cc_final: 0.9185 (t0) REVERT: E 56 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7840 (p90) REVERT: E 262 ASN cc_start: 0.8785 (t0) cc_final: 0.8495 (t0) REVERT: F 92 VAL cc_start: 0.9282 (t) cc_final: 0.9025 (p) REVERT: F 140 LYS cc_start: 0.7540 (ptpt) cc_final: 0.6568 (tmmt) REVERT: F 142 ASN cc_start: 0.9299 (p0) cc_final: 0.8496 (p0) REVERT: F 172 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7865 (mt-10) REVERT: G 41 MET cc_start: 0.9376 (tpt) cc_final: 0.9072 (mmm) REVERT: G 131 ARG cc_start: 0.8354 (ppt170) cc_final: 0.8032 (tmt170) REVERT: H 898 PHE cc_start: 0.7311 (t80) cc_final: 0.7106 (t80) REVERT: I 893 VAL cc_start: 0.8649 (t) cc_final: 0.8437 (p) REVERT: I 897 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7489 (tp30) REVERT: K 895 TYR cc_start: 0.8947 (m-80) cc_final: 0.8692 (m-80) outliers start: 49 outliers final: 31 residues processed: 175 average time/residue: 0.3133 time to fit residues: 87.0640 Evaluate side-chains 161 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR 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 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 249 LEU Chi-restraints excluded: chain G residue 305 LEU 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: 0.0040 chunk 140 optimal weight: 0.5980 chunk 62 optimal weight: 0.0470 chunk 115 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 199 optimal weight: 0.0470 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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** E 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058314 restraints weight = 56274.559| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.64 r_work: 0.2835 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1921 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= 0.090 Angle : 0.469 9.682 28544 Z= 0.233 Chirality : 0.038 0.137 3197 Planarity : 0.003 0.046 3523 Dihedral : 12.631 104.686 3278 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.95 % Allowed : 15.71 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.18), residues: 2407 helix: 1.93 (0.14), residues: 1442 sheet: 0.20 (0.40), residues: 196 loop : 0.55 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.005 0.000 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 0.03174 ( 1078) hydrogen bonds : angle 3.35069 ( 2933) covalent geometry : bond 0.00191 (20955) covalent geometry : angle 0.46862 (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 182 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8455 (p90) cc_final: 0.8179 (t80) REVERT: A 142 ASN cc_start: 0.8213 (m110) cc_final: 0.7765 (m110) REVERT: A 164 HIS cc_start: 0.8836 (t-90) cc_final: 0.8108 (t-90) REVERT: A 198 MET cc_start: 0.7922 (mtm) cc_final: 0.7408 (ptp) REVERT: A 221 LEU cc_start: 0.3598 (OUTLIER) cc_final: 0.3356 (mt) REVERT: B 73 LYS cc_start: 0.9025 (tptm) cc_final: 0.8546 (tppt) REVERT: B 227 ASP cc_start: 0.8783 (m-30) cc_final: 0.8357 (p0) REVERT: C 34 LYS cc_start: 0.9327 (mmmt) cc_final: 0.8898 (mtpt) REVERT: C 121 LEU cc_start: 0.8859 (mp) cc_final: 0.8529 (pp) REVERT: C 137 ASN cc_start: 0.8967 (t0) cc_final: 0.8591 (t0) REVERT: C 198 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: C 221 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (mm) REVERT: C 286 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8431 (tptp) REVERT: D 24 GLU cc_start: 0.9325 (tp30) cc_final: 0.8907 (tp30) REVERT: D 41 MET cc_start: 0.8986 (mmm) cc_final: 0.8755 (mmm) REVERT: D 142 ASN cc_start: 0.9087 (m-40) cc_final: 0.8215 (p0) REVERT: E 56 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7791 (p90) REVERT: E 94 ILE cc_start: 0.8995 (tp) cc_final: 0.8730 (pt) REVERT: E 105 ASN cc_start: 0.9080 (t0) cc_final: 0.8850 (t0) REVERT: E 262 ASN cc_start: 0.8802 (t0) cc_final: 0.8490 (t0) REVERT: F 92 VAL cc_start: 0.9290 (t) cc_final: 0.9054 (p) REVERT: F 119 GLU cc_start: 0.6920 (tp30) cc_final: 0.6482 (pm20) REVERT: F 140 LYS cc_start: 0.7493 (ptpt) cc_final: 0.6462 (tmmt) REVERT: F 142 ASN cc_start: 0.9260 (p0) cc_final: 0.8448 (p0) REVERT: F 172 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7734 (mt-10) REVERT: G 41 MET cc_start: 0.9374 (tpt) cc_final: 0.9072 (mmm) REVERT: G 131 ARG cc_start: 0.8393 (ppt170) cc_final: 0.8033 (tmt170) REVERT: H 898 PHE cc_start: 0.7287 (t80) cc_final: 0.7080 (t80) REVERT: I 897 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7515 (tp30) outliers start: 41 outliers final: 20 residues processed: 173 average time/residue: 0.3168 time to fit residues: 86.5295 Evaluate side-chains 153 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 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 286 LYS Chi-restraints excluded: chain D residue 9 LEU 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 248 LEU 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 249 LEU Chi-restraints excluded: chain G residue 305 LEU 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: 1.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 B 220 GLN E 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.080690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056198 restraints weight = 56312.185| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.62 r_work: 0.2809 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20955 Z= 0.131 Angle : 0.496 9.707 28544 Z= 0.247 Chirality : 0.039 0.299 3197 Planarity : 0.003 0.044 3523 Dihedral : 12.568 101.965 3277 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.33 % Allowed : 15.71 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.18), residues: 2407 helix: 1.92 (0.14), residues: 1451 sheet: 0.18 (0.40), residues: 196 loop : 0.54 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.027 0.001 TYR G 110 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 1078) hydrogen bonds : angle 3.40041 ( 2933) covalent geometry : bond 0.00300 (20955) covalent geometry : angle 0.49606 (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 180 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8487 (p90) cc_final: 0.8198 (t80) REVERT: A 142 ASN cc_start: 0.8176 (m110) cc_final: 0.7730 (m110) REVERT: A 164 HIS cc_start: 0.8852 (t-90) cc_final: 0.8120 (t-90) REVERT: A 198 MET cc_start: 0.7896 (mtm) cc_final: 0.7373 (ptp) REVERT: A 221 LEU cc_start: 0.3564 (OUTLIER) cc_final: 0.3284 (mt) REVERT: B 73 LYS cc_start: 0.9046 (tptm) cc_final: 0.8614 (tppt) REVERT: B 137 ASN cc_start: 0.7705 (t0) cc_final: 0.7164 (p0) REVERT: B 227 ASP cc_start: 0.8776 (m-30) cc_final: 0.8392 (p0) REVERT: C 34 LYS cc_start: 0.9350 (mmmt) cc_final: 0.8924 (mtpt) REVERT: C 121 LEU cc_start: 0.8879 (mp) cc_final: 0.8554 (pp) REVERT: C 137 ASN cc_start: 0.9002 (t0) cc_final: 0.8643 (p0) REVERT: C 198 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8218 (mtp) REVERT: C 221 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8836 (mm) REVERT: D 24 GLU cc_start: 0.9335 (tp30) cc_final: 0.8924 (tp30) REVERT: D 41 MET cc_start: 0.8997 (mmm) cc_final: 0.8751 (mmm) REVERT: D 142 ASN cc_start: 0.9093 (m-40) cc_final: 0.8228 (p0) REVERT: E 56 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7773 (p90) REVERT: E 94 ILE cc_start: 0.8987 (tp) cc_final: 0.8673 (pt) REVERT: E 262 ASN cc_start: 0.8801 (t0) cc_final: 0.8525 (t0) REVERT: F 92 VAL cc_start: 0.9271 (t) cc_final: 0.9019 (p) REVERT: F 140 LYS cc_start: 0.7537 (ptpt) cc_final: 0.6480 (tmmt) REVERT: F 142 ASN cc_start: 0.9277 (p0) cc_final: 0.8468 (p0) REVERT: F 172 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7834 (mt-10) REVERT: G 41 MET cc_start: 0.9376 (tpt) cc_final: 0.9085 (tpt) REVERT: G 131 ARG cc_start: 0.8409 (ppt170) cc_final: 0.8040 (tmt170) REVERT: G 176 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7299 (t80) outliers start: 49 outliers final: 30 residues processed: 171 average time/residue: 0.3077 time to fit residues: 83.0264 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 : 2.361 ------------------------------------------------------------------------------- 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 299 THR 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 298 THR 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 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 103 TYR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU 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: 0.1980 chunk 1 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 232 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 25 ASN B 197 ASN B 220 GLN ** E 162 HIS ** 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 = 0.3495 r_free = 0.3495 target = 0.081530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057179 restraints weight = 55970.176| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.61 r_work: 0.2811 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20955 Z= 0.098 Angle : 0.477 9.818 28544 Z= 0.237 Chirality : 0.038 0.211 3197 Planarity : 0.003 0.043 3523 Dihedral : 12.489 99.412 3276 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.95 % Allowed : 16.75 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.18), residues: 2407 helix: 1.94 (0.14), residues: 1450 sheet: 0.18 (0.40), residues: 196 loop : 0.55 (0.25), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.025 0.001 TYR G 110 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 1078) hydrogen bonds : angle 3.31717 ( 2933) covalent geometry : bond 0.00218 (20955) covalent geometry : angle 0.47683 (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 171 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8477 (p90) cc_final: 0.8220 (t80) REVERT: A 142 ASN cc_start: 0.8209 (m110) cc_final: 0.7795 (m110) REVERT: A 164 HIS cc_start: 0.8869 (t-90) cc_final: 0.8130 (t-90) REVERT: A 198 MET cc_start: 0.7885 (mtm) cc_final: 0.7369 (ptp) REVERT: A 221 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.3302 (mt) REVERT: B 73 LYS cc_start: 0.9033 (tptm) cc_final: 0.8556 (tppt) REVERT: B 137 ASN cc_start: 0.7748 (t0) cc_final: 0.7244 (p0) REVERT: B 227 ASP cc_start: 0.8750 (m-30) cc_final: 0.8385 (p0) REVERT: C 34 LYS cc_start: 0.9347 (mmmt) cc_final: 0.8922 (mtpt) REVERT: C 121 LEU cc_start: 0.8859 (mp) cc_final: 0.8535 (pp) REVERT: C 137 ASN cc_start: 0.8976 (t0) cc_final: 0.8616 (t0) REVERT: C 198 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: C 221 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8819 (mm) REVERT: C 286 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8417 (tptp) REVERT: D 24 GLU cc_start: 0.9322 (tp30) cc_final: 0.8902 (tp30) REVERT: D 41 MET cc_start: 0.8998 (mmm) cc_final: 0.8759 (mmm) REVERT: D 105 ASN cc_start: 0.9406 (OUTLIER) cc_final: 0.9008 (t0) REVERT: D 142 ASN cc_start: 0.9084 (m-40) cc_final: 0.8248 (p0) REVERT: E 56 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7784 (p90) REVERT: E 94 ILE cc_start: 0.8988 (tp) cc_final: 0.8705 (pt) REVERT: E 105 ASN cc_start: 0.9049 (t0) cc_final: 0.8720 (t0) REVERT: E 262 ASN cc_start: 0.8829 (t0) cc_final: 0.8566 (t0) REVERT: F 92 VAL cc_start: 0.9284 (t) cc_final: 0.9047 (p) REVERT: F 119 GLU cc_start: 0.6950 (tp30) cc_final: 0.6447 (pm20) REVERT: F 140 LYS cc_start: 0.7525 (ptpt) cc_final: 0.6439 (tmmt) REVERT: F 142 ASN cc_start: 0.9247 (p0) cc_final: 0.8433 (p0) REVERT: F 172 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7788 (mt-10) REVERT: G 41 MET cc_start: 0.9377 (tpt) cc_final: 0.9081 (tpt) REVERT: G 95 GLU cc_start: 0.8582 (tt0) cc_final: 0.8140 (tm-30) REVERT: G 131 ARG cc_start: 0.8425 (ppt170) cc_final: 0.8032 (tmt170) REVERT: G 176 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7231 (t80) outliers start: 41 outliers final: 27 residues processed: 164 average time/residue: 0.3111 time to fit residues: 81.3714 Evaluate side-chains 158 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 298 THR Chi-restraints excluded: chain C residue 28 VAL 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 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 105 ASN 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 237 SER Chi-restraints excluded: chain F residue 248 LEU 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 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 59 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 234 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056982 restraints weight = 56324.912| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.59 r_work: 0.2804 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20955 Z= 0.107 Angle : 0.479 9.797 28544 Z= 0.238 Chirality : 0.038 0.161 3197 Planarity : 0.003 0.043 3523 Dihedral : 12.428 95.655 3276 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.00 % Allowed : 16.99 % 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: 2.00 (0.18), residues: 2407 helix: 1.96 (0.14), residues: 1450 sheet: 0.19 (0.40), residues: 196 loop : 0.54 (0.25), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.020 0.001 TYR G 110 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 1078) hydrogen bonds : angle 3.30612 ( 2933) covalent geometry : bond 0.00240 (20955) covalent geometry : angle 0.47928 (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 170 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8469 (p90) cc_final: 0.8229 (t80) REVERT: A 142 ASN cc_start: 0.8208 (m110) cc_final: 0.7802 (m110) REVERT: A 164 HIS cc_start: 0.8864 (t-90) cc_final: 0.8112 (t-90) REVERT: A 198 MET cc_start: 0.7882 (mtm) cc_final: 0.7429 (ptp) REVERT: A 221 LEU cc_start: 0.3621 (OUTLIER) cc_final: 0.3361 (mt) REVERT: B 73 LYS cc_start: 0.9031 (tptm) cc_final: 0.8555 (tppt) REVERT: B 142 ASN cc_start: 0.8381 (t0) cc_final: 0.8117 (t0) REVERT: B 227 ASP cc_start: 0.8753 (m-30) cc_final: 0.8379 (p0) REVERT: C 34 LYS cc_start: 0.9354 (mmmt) cc_final: 0.8930 (mtpt) REVERT: C 103 TYR cc_start: 0.8374 (p90) cc_final: 0.8101 (p90) REVERT: C 121 LEU cc_start: 0.8869 (mp) cc_final: 0.8539 (pp) REVERT: C 137 ASN cc_start: 0.8988 (t0) cc_final: 0.8662 (p0) REVERT: C 198 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: C 221 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8816 (mm) REVERT: D 24 GLU cc_start: 0.9328 (tp30) cc_final: 0.8917 (tp30) REVERT: D 41 MET cc_start: 0.9003 (mmm) cc_final: 0.8766 (mmm) REVERT: D 142 ASN cc_start: 0.9091 (m-40) cc_final: 0.8279 (p0) REVERT: E 56 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7814 (p90) REVERT: E 94 ILE cc_start: 0.8979 (tp) cc_final: 0.8702 (pt) REVERT: E 105 ASN cc_start: 0.9028 (t0) cc_final: 0.8657 (t0) REVERT: E 262 ASN cc_start: 0.8833 (t0) cc_final: 0.8610 (t0) REVERT: F 92 VAL cc_start: 0.9271 (t) cc_final: 0.9033 (p) REVERT: F 140 LYS cc_start: 0.7539 (ptpt) cc_final: 0.6582 (tmmt) REVERT: F 172 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7795 (mt-10) REVERT: G 41 MET cc_start: 0.9371 (tpt) cc_final: 0.9057 (mmm) REVERT: G 131 ARG cc_start: 0.8428 (ppt170) cc_final: 0.8051 (tmt170) REVERT: G 176 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7208 (t80) REVERT: I 897 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7754 (tt0) outliers start: 42 outliers final: 30 residues processed: 163 average time/residue: 0.3094 time to fit residues: 79.8496 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 160 optimal weight: 0.7980 chunk 233 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 25 ASN B 197 ASN B 220 GLN ** E 162 HIS ** 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 = 0.3494 r_free = 0.3494 target = 0.081503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057343 restraints weight = 56157.664| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.59 r_work: 0.2812 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2379 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= 0.099 Angle : 0.482 9.980 28544 Z= 0.238 Chirality : 0.038 0.314 3197 Planarity : 0.003 0.049 3523 Dihedral : 12.352 89.785 3276 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 17.09 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.18), residues: 2407 helix: 1.98 (0.14), residues: 1450 sheet: 0.31 (0.46), residues: 131 loop : 0.37 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.020 0.001 TYR G 110 ARG 0.004 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 1078) hydrogen bonds : angle 3.27855 ( 2933) covalent geometry : bond 0.00221 (20955) covalent geometry : angle 0.48191 (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 176 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8214 (m110) cc_final: 0.7821 (m110) REVERT: A 164 HIS cc_start: 0.8882 (t-90) cc_final: 0.8129 (t-90) REVERT: A 198 MET cc_start: 0.8018 (mtm) cc_final: 0.7464 (ptp) REVERT: A 221 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3386 (mt) REVERT: B 73 LYS cc_start: 0.9036 (tptm) cc_final: 0.8547 (tppt) REVERT: B 142 ASN cc_start: 0.8397 (t0) cc_final: 0.8131 (t0) REVERT: B 227 ASP cc_start: 0.8731 (m-30) cc_final: 0.8359 (p0) REVERT: C 34 LYS cc_start: 0.9354 (mmmt) cc_final: 0.8934 (mtpt) REVERT: C 56 TYR cc_start: 0.8708 (m-80) cc_final: 0.8296 (m-80) REVERT: C 103 TYR cc_start: 0.8368 (p90) cc_final: 0.8106 (p90) REVERT: C 121 LEU cc_start: 0.8870 (mp) cc_final: 0.8543 (pp) REVERT: C 137 ASN cc_start: 0.8999 (t0) cc_final: 0.8657 (t0) REVERT: C 198 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: C 221 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8801 (mm) REVERT: C 286 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8418 (tptp) REVERT: D 24 GLU cc_start: 0.9322 (tp30) cc_final: 0.8906 (tp30) REVERT: D 41 MET cc_start: 0.8997 (mmm) cc_final: 0.8760 (mmm) REVERT: D 105 ASN cc_start: 0.9404 (OUTLIER) cc_final: 0.9024 (t0) REVERT: D 142 ASN cc_start: 0.9092 (m-40) cc_final: 0.8318 (p0) REVERT: D 144 GLU cc_start: 0.8679 (tp30) cc_final: 0.8275 (mt-10) REVERT: E 56 TYR cc_start: 0.8549 (p90) cc_final: 0.7809 (p90) REVERT: E 94 ILE cc_start: 0.8954 (tp) cc_final: 0.8695 (pt) REVERT: E 105 ASN cc_start: 0.9027 (t0) cc_final: 0.8638 (t0) REVERT: E 262 ASN cc_start: 0.8822 (t0) cc_final: 0.8607 (t0) REVERT: F 92 VAL cc_start: 0.9266 (t) cc_final: 0.9030 (p) REVERT: F 140 LYS cc_start: 0.7551 (ptpt) cc_final: 0.6554 (tmmt) REVERT: G 41 MET cc_start: 0.9380 (tpt) cc_final: 0.9060 (mmm) REVERT: G 95 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: G 131 ARG cc_start: 0.8425 (ppt170) cc_final: 0.8049 (tmt170) REVERT: G 176 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7208 (t80) REVERT: I 897 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7789 (tt0) outliers start: 42 outliers final: 32 residues processed: 168 average time/residue: 0.3131 time to fit residues: 83.0451 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 : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 105 ASN Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 3 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 181 optimal weight: 0.0070 chunk 66 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 216 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057714 restraints weight = 56262.026| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.58 r_work: 0.2821 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20955 Z= 0.095 Angle : 0.487 9.846 28544 Z= 0.240 Chirality : 0.039 0.293 3197 Planarity : 0.003 0.050 3523 Dihedral : 12.270 84.057 3274 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 17.61 % 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: 1.99 (0.18), residues: 2407 helix: 2.00 (0.14), residues: 1450 sheet: 0.37 (0.46), residues: 131 loop : 0.36 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP F 284 HIS 0.005 0.000 HIS G 30 PHE 0.012 0.001 PHE F 138 TYR 0.020 0.001 TYR G 110 ARG 0.003 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 1078) hydrogen bonds : angle 3.27801 ( 2933) covalent geometry : bond 0.00211 (20955) covalent geometry : angle 0.48688 (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 169 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8203 (m110) cc_final: 0.7819 (m110) REVERT: A 164 HIS cc_start: 0.8881 (t-90) cc_final: 0.8126 (t-90) REVERT: A 198 MET cc_start: 0.7995 (mtm) cc_final: 0.7451 (ptp) REVERT: A 221 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3414 (mt) REVERT: B 73 LYS cc_start: 0.9008 (tptm) cc_final: 0.8502 (tppt) REVERT: B 142 ASN cc_start: 0.8405 (t0) cc_final: 0.8137 (t0) REVERT: B 227 ASP cc_start: 0.8739 (m-30) cc_final: 0.8351 (p0) REVERT: C 34 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9005 (mtpt) REVERT: C 103 TYR cc_start: 0.8338 (p90) cc_final: 0.8087 (p90) REVERT: C 121 LEU cc_start: 0.8874 (mp) cc_final: 0.8537 (pp) REVERT: C 137 ASN cc_start: 0.8975 (t0) cc_final: 0.8622 (t0) REVERT: C 198 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: C 221 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8804 (mm) REVERT: C 286 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8395 (tptp) REVERT: D 24 GLU cc_start: 0.9317 (tp30) cc_final: 0.8902 (tp30) REVERT: D 41 MET cc_start: 0.8979 (mmm) cc_final: 0.8743 (mmm) REVERT: D 105 ASN cc_start: 0.9392 (OUTLIER) cc_final: 0.9010 (t0) REVERT: D 119 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7491 (mt-10) REVERT: D 142 ASN cc_start: 0.9092 (m-40) cc_final: 0.8349 (p0) REVERT: D 144 GLU cc_start: 0.8487 (tp30) cc_final: 0.8107 (mm-30) REVERT: E 56 TYR cc_start: 0.8528 (p90) cc_final: 0.7736 (p90) REVERT: E 94 ILE cc_start: 0.8953 (tp) cc_final: 0.8696 (pt) REVERT: E 105 ASN cc_start: 0.9022 (t0) cc_final: 0.8603 (t0) REVERT: E 121 LEU cc_start: 0.7451 (tt) cc_final: 0.6897 (pt) REVERT: E 262 ASN cc_start: 0.8808 (t0) cc_final: 0.8582 (t0) REVERT: F 92 VAL cc_start: 0.9254 (t) cc_final: 0.9016 (p) REVERT: F 140 LYS cc_start: 0.7565 (ptpt) cc_final: 0.6368 (tmmt) REVERT: F 142 ASN cc_start: 0.9191 (p0) cc_final: 0.8476 (p0) REVERT: G 41 MET cc_start: 0.9376 (tpt) cc_final: 0.9056 (mmm) REVERT: G 131 ARG cc_start: 0.8427 (ppt170) cc_final: 0.8047 (tmt170) REVERT: G 176 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7136 (t80) REVERT: I 897 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7780 (tt0) outliers start: 38 outliers final: 29 residues processed: 162 average time/residue: 0.3154 time to fit residues: 80.6183 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 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 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 105 ASN Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 103 TYR 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 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 111 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 148 optimal weight: 0.0770 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 197 ASN B 220 GLN ** E 162 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.081594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057516 restraints weight = 56468.394| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.59 r_work: 0.2840 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20955 Z= 0.101 Angle : 0.495 10.189 28544 Z= 0.244 Chirality : 0.039 0.286 3197 Planarity : 0.003 0.078 3523 Dihedral : 12.236 78.018 3274 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.09 % Allowed : 17.28 % 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: 2.00 (0.18), residues: 2407 helix: 2.01 (0.14), residues: 1450 sheet: 0.36 (0.47), residues: 131 loop : 0.36 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP F 284 HIS 0.004 0.000 HIS G 30 PHE 0.018 0.001 PHE D 319 TYR 0.021 0.001 TYR G 110 ARG 0.003 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 1078) hydrogen bonds : angle 3.26731 ( 2933) covalent geometry : bond 0.00229 (20955) covalent geometry : angle 0.49475 (28544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8927.74 seconds wall clock time: 156 minutes 34.04 seconds (9394.04 seconds total)