Starting phenix.real_space_refine on Thu Sep 18 22:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmz_51458/09_2025/9gmz_51458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmz_51458/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gmz_51458/09_2025/9gmz_51458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmz_51458/09_2025/9gmz_51458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gmz_51458/09_2025/9gmz_51458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmz_51458/09_2025/9gmz_51458.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12902 2.51 5 N 3571 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20472 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2688 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "C" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "G" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "1" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.23 Number of scatterers: 20472 At special positions: 0 Unit cell: (97.5, 150.8, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 51 15.00 Mg 7 11.99 O 3885 8.00 N 3571 7.00 C 12902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4604 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 10 sheets defined 63.3% alpha, 6.7% beta 16 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.48 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: 3.67 Time building geometry restraints manager: 2.42 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: 10.170 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: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.810 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2407 helix: 1.71 (0.14), residues: 1430 sheet: 0.44 (0.40), residues: 196 loop : 0.29 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.034 0.001 TYR G 110 PHE 0.038 0.001 PHE G 126 TRP 0.006 0.001 TRP C 284 HIS 0.003 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00344 (20955) covalent geometry : angle 0.64412 (28544) hydrogen bonds : bond 0.16020 ( 1078) hydrogen bonds : angle 4.63898 ( 2933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.834 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: 0.1492 time to fit residues: 43.1217 Evaluate side-chains 158 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 203 HIS D 242 GLN E 216 ASN E 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.055223 restraints weight = 56600.185| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.61 r_work: 0.2787 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20955 Z= 0.224 Angle : 0.601 10.580 28544 Z= 0.304 Chirality : 0.042 0.212 3197 Planarity : 0.004 0.047 3523 Dihedral : 13.255 118.464 3301 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.81 % Allowed : 14.90 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2407 helix: 1.53 (0.14), residues: 1465 sheet: 0.23 (0.39), residues: 196 loop : 0.55 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 308 TYR 0.017 0.001 TYR A 103 PHE 0.028 0.002 PHE L 898 TRP 0.015 0.001 TRP F 284 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00516 (20955) covalent geometry : angle 0.60064 (28544) hydrogen bonds : bond 0.04506 ( 1078) hydrogen bonds : angle 3.91692 ( 2933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 140 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8478 (p90) cc_final: 0.8119 (t80) REVERT: A 142 ASN cc_start: 0.8098 (m110) cc_final: 0.7643 (m110) REVERT: A 164 HIS cc_start: 0.8763 (t-90) cc_final: 0.8109 (t-90) REVERT: A 198 MET cc_start: 0.7924 (mtm) cc_final: 0.7432 (ptp) REVERT: A 328 GLN cc_start: 0.8326 (mt0) cc_final: 0.8049 (mp10) REVERT: B 137 ASN cc_start: 0.7809 (t0) cc_final: 0.7321 (p0) REVERT: B 220 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: B 227 ASP cc_start: 0.8835 (m-30) cc_final: 0.8369 (p0) REVERT: C 34 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9013 (mtpt) REVERT: C 69 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8520 (tpp80) REVERT: C 121 LEU cc_start: 0.8915 (mp) cc_final: 0.8610 (pp) REVERT: C 137 ASN cc_start: 0.8980 (t0) cc_final: 0.8580 (t0) REVERT: C 221 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 307 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8912 (tppt) REVERT: D 24 GLU cc_start: 0.9363 (tp30) cc_final: 0.8970 (tp30) REVERT: D 153 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8115 (ttt180) REVERT: D 291 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.9207 (t0) REVERT: E 56 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7870 (p90) REVERT: E 102 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.7614 (ttp-110) REVERT: E 262 ASN cc_start: 0.8801 (t0) cc_final: 0.8548 (t0) REVERT: F 94 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8895 (pt) REVERT: F 140 LYS cc_start: 0.7545 (ptpt) cc_final: 0.6624 (tmmt) REVERT: F 142 ASN cc_start: 0.9310 (p0) cc_final: 0.8509 (p0) REVERT: F 172 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8038 (mt-10) REVERT: F 248 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8690 (mm) REVERT: G 41 MET cc_start: 0.9384 (tpt) cc_final: 0.9105 (tpt) REVERT: G 131 ARG cc_start: 0.8396 (ppt170) cc_final: 0.8039 (tmt170) REVERT: G 271 TYR cc_start: 0.7900 (t80) cc_final: 0.7538 (t80) REVERT: G 303 LYS cc_start: 0.9113 (tppt) cc_final: 0.8910 (mmtp) REVERT: H 898 PHE cc_start: 0.7281 (t80) cc_final: 0.6961 (t80) REVERT: I 893 VAL cc_start: 0.8508 (t) cc_final: 0.8224 (p) REVERT: I 897 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7439 (tp30) REVERT: J 895 TYR cc_start: 0.8931 (m-80) cc_final: 0.8699 (m-80) REVERT: M 893 VAL cc_start: 0.8392 (m) cc_final: 0.8183 (p) outliers start: 59 outliers final: 28 residues processed: 186 average time/residue: 0.1524 time to fit residues: 43.1969 Evaluate side-chains 165 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 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 153 ARG 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 152 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 E 216 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054832 restraints weight = 56663.560| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.61 r_work: 0.2773 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20955 Z= 0.173 Angle : 0.536 8.392 28544 Z= 0.270 Chirality : 0.040 0.136 3197 Planarity : 0.004 0.057 3523 Dihedral : 13.062 114.785 3292 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 14.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.18), residues: 2407 helix: 1.53 (0.14), residues: 1470 sheet: 0.11 (0.39), residues: 196 loop : 0.43 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 14 TYR 0.030 0.001 TYR G 110 PHE 0.015 0.001 PHE D 319 TRP 0.012 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00399 (20955) covalent geometry : angle 0.53600 (28544) hydrogen bonds : bond 0.03984 ( 1078) hydrogen bonds : angle 3.66878 ( 2933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8455 (p90) cc_final: 0.8127 (t80) REVERT: A 142 ASN cc_start: 0.8135 (m110) cc_final: 0.7659 (m110) REVERT: A 164 HIS cc_start: 0.8817 (t-90) cc_final: 0.8109 (t-90) REVERT: A 198 MET cc_start: 0.7886 (mtm) cc_final: 0.7387 (ptp) REVERT: A 328 GLN cc_start: 0.8306 (mt0) cc_final: 0.8032 (mp10) REVERT: B 73 LYS cc_start: 0.9077 (tptm) cc_final: 0.8637 (tppt) REVERT: B 137 ASN cc_start: 0.7850 (t0) cc_final: 0.7443 (p0) REVERT: B 220 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7822 (tp40) REVERT: B 227 ASP cc_start: 0.8840 (m-30) cc_final: 0.8395 (p0) REVERT: C 34 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9027 (mtpt) REVERT: C 69 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8391 (tpp80) REVERT: C 121 LEU cc_start: 0.8897 (mp) cc_final: 0.8589 (pp) REVERT: C 137 ASN cc_start: 0.8971 (t0) cc_final: 0.8632 (t0) REVERT: C 221 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8876 (mm) REVERT: D 142 ASN cc_start: 0.9063 (m-40) cc_final: 0.8153 (p0) REVERT: E 56 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7996 (p90) REVERT: E 94 ILE cc_start: 0.9004 (tp) cc_final: 0.8670 (pt) REVERT: F 92 VAL cc_start: 0.9281 (t) cc_final: 0.9004 (p) REVERT: F 140 LYS cc_start: 0.7591 (ptpt) cc_final: 0.6796 (tmmt) REVERT: F 172 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7960 (mt-10) REVERT: F 248 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8670 (mm) REVERT: G 131 ARG cc_start: 0.8428 (ppt170) cc_final: 0.8055 (tmt170) REVERT: G 176 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7314 (t80) REVERT: G 271 TYR cc_start: 0.7838 (t80) cc_final: 0.7541 (t80) REVERT: I 893 VAL cc_start: 0.8786 (t) cc_final: 0.8540 (p) REVERT: I 897 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7518 (tp30) REVERT: K 895 TYR cc_start: 0.8967 (m-80) cc_final: 0.8698 (m-80) outliers start: 54 outliers final: 25 residues processed: 179 average time/residue: 0.1379 time to fit residues: 38.2193 Evaluate side-chains 155 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 219 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN G 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.080087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055498 restraints weight = 56510.487| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.61 r_work: 0.2765 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20955 Z= 0.125 Angle : 0.501 9.719 28544 Z= 0.250 Chirality : 0.039 0.238 3197 Planarity : 0.003 0.055 3523 Dihedral : 12.904 110.216 3284 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.62 % Allowed : 15.47 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2407 helix: 1.65 (0.14), residues: 1462 sheet: 0.06 (0.39), residues: 196 loop : 0.48 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 153 TYR 0.030 0.001 TYR G 110 PHE 0.014 0.001 PHE F 138 TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00285 (20955) covalent geometry : angle 0.50105 (28544) hydrogen bonds : bond 0.03606 ( 1078) hydrogen bonds : angle 3.54076 ( 2933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8460 (p90) cc_final: 0.8136 (t80) REVERT: A 142 ASN cc_start: 0.8130 (m110) cc_final: 0.7695 (m110) REVERT: A 164 HIS cc_start: 0.8833 (t-90) cc_final: 0.8122 (t-90) REVERT: A 198 MET cc_start: 0.7868 (mtm) cc_final: 0.7366 (ptp) REVERT: B 73 LYS cc_start: 0.9059 (tptm) cc_final: 0.8627 (tppt) REVERT: B 137 ASN cc_start: 0.7847 (t0) cc_final: 0.7501 (p0) REVERT: B 220 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7827 (tp40) REVERT: B 227 ASP cc_start: 0.8797 (m-30) cc_final: 0.8424 (p0) REVERT: C 34 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9022 (mtpt) REVERT: C 69 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8371 (tpp80) REVERT: C 121 LEU cc_start: 0.8883 (mp) cc_final: 0.8567 (pp) REVERT: C 137 ASN cc_start: 0.9006 (t0) cc_final: 0.8616 (t0) REVERT: C 221 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 142 ASN cc_start: 0.9063 (m-40) cc_final: 0.8134 (p0) REVERT: D 166 ASP cc_start: 0.9379 (OUTLIER) cc_final: 0.9168 (m-30) REVERT: E 56 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7894 (p90) REVERT: E 94 ILE cc_start: 0.8978 (tp) cc_final: 0.8658 (pt) REVERT: E 105 ASN cc_start: 0.9061 (t0) cc_final: 0.8802 (t0) REVERT: F 92 VAL cc_start: 0.9281 (t) cc_final: 0.9025 (p) REVERT: F 140 LYS cc_start: 0.7563 (ptpt) cc_final: 0.6660 (tmmt) REVERT: F 142 ASN cc_start: 0.9322 (p0) cc_final: 0.8848 (p0) REVERT: F 172 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7889 (mt-10) REVERT: G 131 ARG cc_start: 0.8442 (ppt170) cc_final: 0.8063 (tmt170) REVERT: G 176 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (t80) REVERT: G 271 TYR cc_start: 0.7803 (t80) cc_final: 0.7524 (t80) REVERT: I 893 VAL cc_start: 0.8824 (t) cc_final: 0.8589 (p) REVERT: I 897 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7539 (tp30) REVERT: K 895 TYR cc_start: 0.8944 (m-80) cc_final: 0.8731 (m-80) outliers start: 55 outliers final: 29 residues processed: 182 average time/residue: 0.1405 time to fit residues: 39.9168 Evaluate side-chains 164 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 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 76 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 67 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 142 optimal weight: 0.0040 chunk 109 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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** F 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056209 restraints weight = 56115.117| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.59 r_work: 0.2785 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2143 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= 0.107 Angle : 0.489 9.470 28544 Z= 0.242 Chirality : 0.039 0.180 3197 Planarity : 0.003 0.050 3523 Dihedral : 12.726 105.264 3282 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 15.75 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2407 helix: 1.84 (0.14), residues: 1452 sheet: 0.11 (0.40), residues: 196 loop : 0.46 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 153 TYR 0.032 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.008 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00241 (20955) covalent geometry : angle 0.48943 (28544) hydrogen bonds : bond 0.03347 ( 1078) hydrogen bonds : angle 3.40528 ( 2933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8479 (p90) cc_final: 0.8183 (t80) REVERT: A 142 ASN cc_start: 0.8182 (m110) cc_final: 0.7771 (m110) REVERT: A 164 HIS cc_start: 0.8859 (t-90) cc_final: 0.8151 (t-90) REVERT: A 198 MET cc_start: 0.7888 (mtm) cc_final: 0.7374 (ptp) REVERT: A 221 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.3319 (mt) REVERT: B 73 LYS cc_start: 0.9054 (tptm) cc_final: 0.8567 (tppt) REVERT: B 137 ASN cc_start: 0.7860 (t0) cc_final: 0.7568 (p0) REVERT: B 142 ASN cc_start: 0.8389 (t0) cc_final: 0.8116 (t0) REVERT: B 172 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8974 (mt-10) REVERT: B 220 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7888 (tp40) REVERT: B 227 ASP cc_start: 0.8759 (m-30) cc_final: 0.8442 (p0) REVERT: C 34 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9027 (mtpt) REVERT: C 69 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8351 (tpp80) REVERT: C 121 LEU cc_start: 0.8856 (mp) cc_final: 0.8550 (pp) REVERT: C 137 ASN cc_start: 0.8979 (t0) cc_final: 0.8621 (t0) REVERT: D 24 GLU cc_start: 0.9342 (tp30) cc_final: 0.8924 (tp30) REVERT: D 142 ASN cc_start: 0.9094 (m-40) cc_final: 0.8207 (p0) REVERT: E 56 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7883 (p90) REVERT: E 94 ILE cc_start: 0.8987 (tp) cc_final: 0.8715 (pt) REVERT: E 105 ASN cc_start: 0.9100 (t0) cc_final: 0.8798 (t0) REVERT: F 92 VAL cc_start: 0.9277 (t) cc_final: 0.9031 (p) REVERT: F 140 LYS cc_start: 0.7581 (ptpt) cc_final: 0.6533 (tmmt) REVERT: F 142 ASN cc_start: 0.9306 (p0) cc_final: 0.8539 (p0) REVERT: F 172 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7850 (mt-10) REVERT: F 248 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8662 (mm) REVERT: G 103 TYR cc_start: 0.7951 (p90) cc_final: 0.7602 (p90) REVERT: G 131 ARG cc_start: 0.8454 (ppt170) cc_final: 0.8064 (tmt170) REVERT: I 897 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7586 (tp30) outliers start: 54 outliers final: 31 residues processed: 180 average time/residue: 0.1339 time to fit residues: 37.5650 Evaluate side-chains 161 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 202 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 F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain I residue 896 GLU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 203 optimal weight: 10.9990 chunk 158 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 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** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055429 restraints weight = 56149.766| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.59 r_work: 0.2790 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2294 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= 0.130 Angle : 0.503 12.183 28544 Z= 0.247 Chirality : 0.039 0.134 3197 Planarity : 0.003 0.055 3523 Dihedral : 12.685 102.673 3282 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 16.61 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.18), residues: 2407 helix: 1.87 (0.14), residues: 1451 sheet: 0.06 (0.40), residues: 196 loop : 0.46 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.031 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00298 (20955) covalent geometry : angle 0.50281 (28544) hydrogen bonds : bond 0.03432 ( 1078) hydrogen bonds : angle 3.42737 ( 2933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8453 (p90) cc_final: 0.8193 (t80) REVERT: A 142 ASN cc_start: 0.8184 (m110) cc_final: 0.7791 (m110) REVERT: A 164 HIS cc_start: 0.8866 (t-90) cc_final: 0.8138 (t-90) REVERT: A 198 MET cc_start: 0.7898 (mtm) cc_final: 0.7375 (ptp) REVERT: A 221 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.3394 (mt) REVERT: B 73 LYS cc_start: 0.9057 (tptm) cc_final: 0.8613 (tppt) REVERT: B 220 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: B 227 ASP cc_start: 0.8766 (m-30) cc_final: 0.8382 (p0) REVERT: C 34 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9028 (mtpt) REVERT: C 69 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8346 (tpp80) REVERT: C 103 TYR cc_start: 0.8377 (p90) cc_final: 0.8051 (p90) REVERT: C 121 LEU cc_start: 0.8877 (mp) cc_final: 0.8569 (pp) REVERT: C 137 ASN cc_start: 0.8974 (t0) cc_final: 0.8632 (t0) REVERT: C 198 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: C 221 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 286 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8453 (tptp) REVERT: D 142 ASN cc_start: 0.9091 (m-40) cc_final: 0.8228 (p0) REVERT: E 56 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7864 (p90) REVERT: E 94 ILE cc_start: 0.8994 (tp) cc_final: 0.8692 (pt) REVERT: E 105 ASN cc_start: 0.9109 (t0) cc_final: 0.8825 (t0) REVERT: F 92 VAL cc_start: 0.9267 (t) cc_final: 0.9015 (p) REVERT: F 140 LYS cc_start: 0.7576 (ptpt) cc_final: 0.6641 (tmmt) REVERT: F 172 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7872 (mt-10) REVERT: F 248 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8652 (mm) REVERT: G 131 ARG cc_start: 0.8447 (ppt170) cc_final: 0.8117 (tmt170) REVERT: G 176 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7179 (t80) REVERT: G 178 LYS cc_start: 0.7039 (mptt) cc_final: 0.6711 (mmtp) REVERT: I 897 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7631 (tp30) outliers start: 52 outliers final: 34 residues processed: 169 average time/residue: 0.1336 time to fit residues: 35.0812 Evaluate side-chains 165 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 192 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056307 restraints weight = 57304.166| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.32 r_work: 0.2793 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20955 Z= 0.136 Angle : 0.505 10.136 28544 Z= 0.250 Chirality : 0.039 0.136 3197 Planarity : 0.003 0.053 3523 Dihedral : 12.606 95.887 3281 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.00 % Allowed : 16.18 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.18), residues: 2407 helix: 1.88 (0.14), residues: 1451 sheet: 0.05 (0.40), residues: 196 loop : 0.41 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.030 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.010 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00312 (20955) covalent geometry : angle 0.50497 (28544) hydrogen bonds : bond 0.03453 ( 1078) hydrogen bonds : angle 3.41552 ( 2933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8337 (m110) cc_final: 0.7973 (m110) REVERT: A 164 HIS cc_start: 0.8883 (t-90) cc_final: 0.8124 (t-90) REVERT: A 198 MET cc_start: 0.7890 (mtm) cc_final: 0.7409 (ptp) REVERT: A 221 LEU cc_start: 0.3651 (OUTLIER) cc_final: 0.3344 (mt) REVERT: B 73 LYS cc_start: 0.9150 (tptm) cc_final: 0.8751 (tppt) REVERT: B 137 ASN cc_start: 0.7667 (t0) cc_final: 0.7151 (p0) REVERT: B 172 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8998 (mt-10) REVERT: B 227 ASP cc_start: 0.8607 (m-30) cc_final: 0.8354 (p0) REVERT: C 34 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9153 (mtpt) REVERT: C 56 TYR cc_start: 0.8747 (m-80) cc_final: 0.8440 (m-80) REVERT: C 103 TYR cc_start: 0.8460 (p90) cc_final: 0.8162 (p90) REVERT: C 121 LEU cc_start: 0.8844 (mp) cc_final: 0.8610 (pp) REVERT: C 137 ASN cc_start: 0.8945 (t0) cc_final: 0.8622 (t0) REVERT: C 221 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (mm) REVERT: C 286 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8507 (tptp) REVERT: D 142 ASN cc_start: 0.9144 (m-40) cc_final: 0.8344 (p0) REVERT: E 56 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8009 (p90) REVERT: F 92 VAL cc_start: 0.9369 (t) cc_final: 0.9163 (p) REVERT: F 140 LYS cc_start: 0.7535 (ptpt) cc_final: 0.6509 (tmmt) REVERT: F 172 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7950 (mt-10) REVERT: F 248 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8825 (mm) REVERT: G 131 ARG cc_start: 0.8487 (ppt170) cc_final: 0.8154 (tmt170) REVERT: G 176 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7237 (t80) REVERT: G 178 LYS cc_start: 0.7056 (mptt) cc_final: 0.6756 (mmtp) REVERT: I 897 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7674 (tp30) REVERT: L 896 GLU cc_start: 0.8605 (mp0) cc_final: 0.8381 (mm-30) outliers start: 63 outliers final: 43 residues processed: 184 average time/residue: 0.1456 time to fit residues: 41.4907 Evaluate side-chains 170 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL 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 C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 202 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 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain 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 G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 157 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 65 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055099 restraints weight = 56262.724| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.46 r_work: 0.2770 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20955 Z= 0.131 Angle : 0.517 13.215 28544 Z= 0.254 Chirality : 0.039 0.151 3197 Planarity : 0.003 0.053 3523 Dihedral : 12.527 90.701 3276 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.71 % Allowed : 16.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.18), residues: 2407 helix: 1.89 (0.14), residues: 1452 sheet: 0.04 (0.40), residues: 196 loop : 0.43 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.033 0.001 TYR G 110 PHE 0.012 0.001 PHE F 138 TRP 0.010 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00304 (20955) covalent geometry : angle 0.51749 (28544) hydrogen bonds : bond 0.03433 ( 1078) hydrogen bonds : angle 3.40766 ( 2933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8275 (m110) cc_final: 0.7910 (m110) REVERT: A 164 HIS cc_start: 0.8885 (t-90) cc_final: 0.8122 (t-90) REVERT: A 198 MET cc_start: 0.8030 (mtm) cc_final: 0.7476 (ptp) REVERT: A 221 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3427 (mt) REVERT: B 73 LYS cc_start: 0.9099 (tptm) cc_final: 0.8672 (tppt) REVERT: B 172 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: B 220 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7745 (tp40) REVERT: B 227 ASP cc_start: 0.8694 (m-30) cc_final: 0.8389 (p0) REVERT: C 34 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9095 (mtpt) REVERT: C 56 TYR cc_start: 0.8767 (m-80) cc_final: 0.8392 (m-80) REVERT: C 121 LEU cc_start: 0.8884 (mp) cc_final: 0.8607 (pp) REVERT: C 137 ASN cc_start: 0.9006 (t0) cc_final: 0.8680 (t0) REVERT: C 198 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8288 (mtp) REVERT: C 221 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8926 (mm) REVERT: C 286 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8499 (tptp) REVERT: D 142 ASN cc_start: 0.9119 (m-40) cc_final: 0.8294 (p0) REVERT: D 144 GLU cc_start: 0.8698 (tp30) cc_final: 0.8321 (mt-10) REVERT: D 166 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9174 (m-30) REVERT: E 56 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7930 (p90) REVERT: E 94 ILE cc_start: 0.9041 (tp) cc_final: 0.8749 (pt) REVERT: F 92 VAL cc_start: 0.9293 (t) cc_final: 0.9053 (p) REVERT: F 140 LYS cc_start: 0.7582 (ptpt) cc_final: 0.6531 (tmmt) REVERT: F 172 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7926 (mt-10) REVERT: F 248 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (mm) REVERT: G 95 GLU cc_start: 0.8662 (tt0) cc_final: 0.8206 (tm-30) REVERT: G 131 ARG cc_start: 0.8481 (ppt170) cc_final: 0.8162 (tmt170) REVERT: G 176 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7189 (t80) REVERT: G 178 LYS cc_start: 0.7041 (mptt) cc_final: 0.6591 (mmtm) REVERT: I 897 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7838 (tt0) outliers start: 57 outliers final: 40 residues processed: 173 average time/residue: 0.1318 time to fit residues: 35.9799 Evaluate side-chains 171 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 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 C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain 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 G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 147 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 217 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 137 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.079973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055907 restraints weight = 55905.633| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.46 r_work: 0.2791 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2629 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= 0.103 Angle : 0.507 13.775 28544 Z= 0.248 Chirality : 0.038 0.215 3197 Planarity : 0.003 0.052 3523 Dihedral : 12.436 85.028 3276 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 17.28 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.18), residues: 2407 helix: 1.91 (0.14), residues: 1452 sheet: 0.11 (0.40), residues: 196 loop : 0.43 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.034 0.001 TYR G 110 PHE 0.012 0.001 PHE F 138 TRP 0.007 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00230 (20955) covalent geometry : angle 0.50667 (28544) hydrogen bonds : bond 0.03298 ( 1078) hydrogen bonds : angle 3.35556 ( 2933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8268 (m110) cc_final: 0.7919 (m110) REVERT: A 164 HIS cc_start: 0.8884 (t-90) cc_final: 0.8112 (t-90) REVERT: A 198 MET cc_start: 0.8042 (mtm) cc_final: 0.7499 (ptp) REVERT: A 221 LEU cc_start: 0.3788 (OUTLIER) cc_final: 0.3483 (mt) REVERT: B 73 LYS cc_start: 0.9088 (tptm) cc_final: 0.8638 (tppt) REVERT: B 172 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8964 (mt-10) REVERT: B 220 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7951 (tp40) REVERT: B 227 ASP cc_start: 0.8673 (m-30) cc_final: 0.8431 (p0) REVERT: C 34 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9087 (mtpt) REVERT: C 56 TYR cc_start: 0.8751 (m-80) cc_final: 0.8367 (m-80) REVERT: C 121 LEU cc_start: 0.8878 (mp) cc_final: 0.8596 (pp) REVERT: C 137 ASN cc_start: 0.9017 (t0) cc_final: 0.8695 (t0) REVERT: C 198 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8295 (mtp) REVERT: C 221 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8893 (mm) REVERT: C 286 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8473 (tptp) REVERT: D 24 GLU cc_start: 0.9319 (tp30) cc_final: 0.8906 (tp30) REVERT: D 142 ASN cc_start: 0.9139 (m-40) cc_final: 0.8350 (p0) REVERT: D 144 GLU cc_start: 0.8575 (tp30) cc_final: 0.8214 (mm-30) REVERT: E 56 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7907 (p90) REVERT: E 94 ILE cc_start: 0.9043 (tp) cc_final: 0.8780 (pt) REVERT: E 121 LEU cc_start: 0.7538 (tt) cc_final: 0.6984 (pt) REVERT: F 92 VAL cc_start: 0.9287 (t) cc_final: 0.9056 (p) REVERT: F 140 LYS cc_start: 0.7574 (ptpt) cc_final: 0.6495 (tmmt) REVERT: G 131 ARG cc_start: 0.8480 (ppt170) cc_final: 0.8160 (tmt170) REVERT: G 176 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7136 (t80) REVERT: G 178 LYS cc_start: 0.7027 (mptt) cc_final: 0.6725 (mmtp) REVERT: G 239 GLU cc_start: 0.8614 (pm20) cc_final: 0.8348 (pm20) REVERT: I 897 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7667 (tp30) REVERT: L 896 GLU cc_start: 0.8660 (mp0) cc_final: 0.8409 (mm-30) outliers start: 47 outliers final: 34 residues processed: 167 average time/residue: 0.1377 time to fit residues: 36.3319 Evaluate side-chains 164 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain 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 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 19 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.080341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056340 restraints weight = 56065.343| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.46 r_work: 0.2803 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2693 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= 0.102 Angle : 0.511 14.682 28544 Z= 0.247 Chirality : 0.038 0.211 3197 Planarity : 0.003 0.051 3523 Dihedral : 12.353 76.958 3276 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 17.42 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.18), residues: 2407 helix: 1.94 (0.14), residues: 1452 sheet: 0.16 (0.46), residues: 131 loop : 0.31 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.019 0.001 TYR G 110 PHE 0.012 0.001 PHE F 138 TRP 0.010 0.001 TRP G 106 HIS 0.005 0.001 HIS G 266 Details of bonding type rmsd covalent geometry : bond 0.00228 (20955) covalent geometry : angle 0.51080 (28544) hydrogen bonds : bond 0.03247 ( 1078) hydrogen bonds : angle 3.31507 ( 2933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8287 (m110) cc_final: 0.7952 (m110) REVERT: A 164 HIS cc_start: 0.8889 (t-90) cc_final: 0.8107 (t-90) REVERT: A 198 MET cc_start: 0.8055 (mtm) cc_final: 0.7517 (ptp) REVERT: A 221 LEU cc_start: 0.3768 (OUTLIER) cc_final: 0.3477 (mt) REVERT: B 73 LYS cc_start: 0.9072 (tptm) cc_final: 0.8625 (tppt) REVERT: B 172 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8940 (mt-10) REVERT: B 227 ASP cc_start: 0.8652 (m-30) cc_final: 0.8408 (p0) REVERT: C 34 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9089 (mtpt) REVERT: C 56 TYR cc_start: 0.8751 (m-80) cc_final: 0.8360 (m-80) REVERT: C 121 LEU cc_start: 0.8878 (mp) cc_final: 0.8583 (pp) REVERT: C 137 ASN cc_start: 0.9028 (t0) cc_final: 0.8707 (t0) REVERT: C 198 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: C 221 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8901 (mm) REVERT: C 286 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8456 (tptp) REVERT: D 24 GLU cc_start: 0.9309 (tp30) cc_final: 0.8901 (tp30) REVERT: D 142 ASN cc_start: 0.9116 (m-40) cc_final: 0.8384 (p0) REVERT: D 144 GLU cc_start: 0.8552 (tp30) cc_final: 0.8068 (mt-10) REVERT: E 56 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7905 (p90) REVERT: E 94 ILE cc_start: 0.9029 (tp) cc_final: 0.8785 (pt) REVERT: E 121 LEU cc_start: 0.7551 (tt) cc_final: 0.6990 (pt) REVERT: F 92 VAL cc_start: 0.9277 (t) cc_final: 0.9052 (p) REVERT: G 131 ARG cc_start: 0.8493 (ppt170) cc_final: 0.8173 (tmt170) REVERT: G 178 LYS cc_start: 0.7043 (mptt) cc_final: 0.6739 (mmtp) REVERT: G 198 MET cc_start: 0.8865 (mtp) cc_final: 0.8656 (mtt) REVERT: G 239 GLU cc_start: 0.8618 (pm20) cc_final: 0.8355 (pm20) REVERT: I 897 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7679 (tp30) outliers start: 42 outliers final: 33 residues processed: 163 average time/residue: 0.1458 time to fit residues: 37.4265 Evaluate side-chains 159 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN D 137 ASN ** 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 = 0.3474 r_free = 0.3474 target = 0.080030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056004 restraints weight = 56004.880| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.45 r_work: 0.2793 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20955 Z= 0.115 Angle : 0.517 14.585 28544 Z= 0.251 Chirality : 0.039 0.211 3197 Planarity : 0.003 0.051 3523 Dihedral : 12.324 75.379 3276 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 17.42 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.18), residues: 2407 helix: 1.77 (0.14), residues: 1487 sheet: 0.12 (0.40), residues: 196 loop : 0.25 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.015 0.001 TYR A 183 PHE 0.015 0.001 PHE C 52 TRP 0.011 0.001 TRP G 106 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00263 (20955) covalent geometry : angle 0.51696 (28544) hydrogen bonds : bond 0.03280 ( 1078) hydrogen bonds : angle 3.32600 ( 2933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4195.49 seconds wall clock time: 72 minutes 59.14 seconds (4379.14 seconds total)