Starting phenix.real_space_refine on Sat Jul 4 10:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0f_50932/07_2026/9g0f_50932.map" } resolution = 3.7 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= 0.007 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 52 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12629 2.51 5 N 3526 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20077 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2672 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} 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: "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: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: 4.99, per 1000 atoms: 0.25 Number of scatterers: 20077 At special positions: 0 Unit cell: (96.2, 152.75, 155.35, 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 52 15.00 Mg 7 11.99 O 3807 8.00 N 3526 7.00 C 12629 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: 1.67 Conformation dependent library (CDL) restraints added in 930.5 milliseconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 10 sheets defined 64.3% alpha, 6.7% beta 16 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.41 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: 4.182A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.509A pdb=" N HIS A 124 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.668A pdb=" N HIS A 175 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.358A pdb=" N GLN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.317A pdb=" N PHE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.874A 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 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' 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: 3.581A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'B' and resid 8 through 14 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 removed outlier: 3.630A pdb=" N TYR B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.619A pdb=" N HIS B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.931A pdb=" N ASP B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.927A pdb=" N THR B 213 " --> pdb=" O GLU B 210 " (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 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' 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 removed outlier: 3.546A pdb=" N ARG B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) 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 removed outlier: 3.864A pdb=" N GLU C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A 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: 4.226A 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: 3.953A pdb=" N ASP C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 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 294 removed outlier: 3.567A pdb=" N LEU C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.740A pdb=" N ARG C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.703A pdb=" N LYS C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.611A pdb=" N GLU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.062A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.645A pdb=" N HIS D 175 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.727A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 4.149A 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: 3.559A pdb=" N ASP D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.564A 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 344 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 85 removed outlier: 4.873A pdb=" N GLU E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 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: 3.833A pdb=" N ASP E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 237 through 255 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 294 removed outlier: 3.682A pdb=" N LEU E 281 " --> pdb=" O CYS E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.743A 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 Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 30 through 45 Processing helix chain 'F' and resid 62 through 79 removed outlier: 3.651A pdb=" N LEU F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.160A pdb=" N GLU F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.882A 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 removed outlier: 3.524A pdb=" N HIS F 175 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.902A pdb=" N ASP F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.959A 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 273 Processing helix chain 'F' and resid 277 through 296 removed outlier: 3.544A pdb=" N LEU F 281 " --> pdb=" O CYS F 277 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O TRP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.528A pdb=" N LYS F 307 " --> pdb=" O LYS F 303 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 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: 3.678A 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: 3.758A pdb=" N LEU G 211 " --> pdb=" O THR G 208 " (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 273 Processing helix chain 'G' and resid 277 through 296 Processing helix chain 'G' and resid 301 through 308 removed outlier: 4.134A pdb=" N ARG G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 330 removed outlier: 3.514A pdb=" N LYS G 320 " --> pdb=" O GLN G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.712A 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: 6.721A pdb=" N VAL A 92 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP A 171 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 94 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.644A pdb=" N VAL B 92 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE B 53 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY B 207 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 55 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 56 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.773A pdb=" N VAL C 92 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP C 171 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 94 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE C 168 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU C 206 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 170 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 207 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.672A pdb=" N VAL D 92 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP D 171 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 94 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 168 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU D 206 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 170 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE D 53 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY D 207 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 55 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 52 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE D 228 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE D 54 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 230 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.633A 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: 6.638A pdb=" N VAL E 92 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP E 171 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 94 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE E 168 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 206 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 170 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE E 53 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY E 207 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 55 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE E 52 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 228 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE E 54 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE E 230 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 56 " --> pdb=" O PHE E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.722A pdb=" N VAL F 92 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP F 171 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 94 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE F 168 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 206 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 170 " --> pdb=" O LEU F 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 92 through 94 removed outlier: 6.331A pdb=" N PHE G 168 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU G 206 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 170 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE G 53 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLY G 207 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL G 55 " --> pdb=" O GLY G 207 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4103 1.33 - 1.45: 4886 1.45 - 1.57: 11403 1.57 - 1.69: 85 1.69 - 1.81: 77 Bond restraints: 20554 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.21e+01 bond pdb=" O3A ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 20549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 27842 4.85 - 9.71: 135 9.71 - 14.56: 17 14.56 - 19.41: 0 19.41 - 24.27: 7 Bond angle restraints: 28001 Sorted by residual: angle pdb=" N ASP C 136 " pdb=" CA ASP C 136 " pdb=" C ASP C 136 " ideal model delta sigma weight residual 113.18 100.72 12.46 1.21e+00 6.83e-01 1.06e+02 angle pdb=" N VAL F 61 " pdb=" CA VAL F 61 " pdb=" C VAL F 61 " ideal model delta sigma weight residual 110.72 119.87 -9.15 1.01e+00 9.80e-01 8.20e+01 angle pdb=" N LYS F 63 " pdb=" CA LYS F 63 " pdb=" C LYS F 63 " ideal model delta sigma weight residual 111.14 120.35 -9.21 1.08e+00 8.57e-01 7.26e+01 angle pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" C VAL E 61 " ideal model delta sigma weight residual 110.72 119.26 -8.54 1.01e+00 9.80e-01 7.16e+01 angle pdb=" PB ANP G 401 " pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 126.95 102.68 24.27 3.00e+00 1.11e-01 6.54e+01 ... (remaining 27996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 11293 24.16 - 48.31: 840 48.31 - 72.47: 201 72.47 - 96.63: 73 96.63 - 120.79: 7 Dihedral angle restraints: 12414 sinusoidal: 5425 harmonic: 6989 Sorted by residual: 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 -133.86 11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA PHE F 214 " pdb=" C PHE F 214 " pdb=" N ARG F 215 " pdb=" CA ARG F 215 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C VAL F 61 " pdb=" N VAL F 61 " pdb=" CA VAL F 61 " pdb=" CB VAL F 61 " ideal model delta harmonic sigma weight residual -122.00 -132.45 10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 12411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2974 0.105 - 0.211: 136 0.211 - 0.316: 17 0.316 - 0.422: 6 0.422 - 0.527: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA VAL F 61 " pdb=" N VAL F 61 " pdb=" C VAL F 61 " pdb=" CB VAL F 61 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU B 345 " pdb=" CB LEU B 345 " pdb=" CD1 LEU B 345 " pdb=" CD2 LEU B 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA LYS F 63 " pdb=" N LYS F 63 " pdb=" C LYS F 63 " pdb=" CB LYS F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 3133 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 21 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ALA E 21 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA E 21 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR E 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 57 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C GLY F 57 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY F 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA F 58 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 135 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C ARG C 135 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG C 135 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP C 136 " -0.015 2.00e-02 2.50e+03 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 134 2.50 - 3.10: 15170 3.10 - 3.70: 31960 3.70 - 4.30: 45154 4.30 - 4.90: 72904 Nonbonded interactions: 165322 Sorted by model distance: nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP C 401 " pdb="MG MG C 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP B 401 " pdb="MG MG B 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP G 401 " pdb="MG MG G 402 " model vdw 1.900 2.170 nonbonded pdb=" O1B ANP A 401 " pdb="MG MG A 402 " model vdw 1.901 2.170 ... (remaining 165317 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 335 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 335 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 335 or resid 401 through 402)) } 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 group one per residue 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: 9.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.430 Find NCS groups from input model: 0.650 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.007 0.159 20554 Z= 0.404 Angle : 0.967 24.267 28001 Z= 0.526 Chirality : 0.055 0.527 3136 Planarity : 0.004 0.051 3454 Dihedral : 18.558 120.785 7898 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 1.17 % Allowed : 12.69 % Favored : 86.14 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2375 helix: 1.14 (0.14), residues: 1453 sheet: 0.54 (0.39), residues: 186 loop : -0.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 112 TYR 0.019 0.001 TYR D 37 PHE 0.015 0.001 PHE A 52 TRP 0.006 0.001 TRP G 284 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.40 (20554) covalent geometry : angle 0.96743 / 0.53 (28001) hydrogen bonds : bond 0.16626 / 11.17 ( 1096) hydrogen bonds : angle 5.64006 / 4.05 ( 2975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9362 (mtm) cc_final: 0.8810 (mtm) REVERT: A 255 LEU cc_start: 0.9467 (pp) cc_final: 0.9241 (pt) REVERT: B 94 ILE cc_start: 0.9180 (tp) cc_final: 0.8901 (tt) REVERT: B 215 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8643 (ttt-90) REVERT: D 41 MET cc_start: 0.9342 (tpp) cc_final: 0.8906 (tpp) REVERT: D 46 GLU cc_start: 0.8678 (tp30) cc_final: 0.8211 (tp30) REVERT: E 59 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.6812 (t) REVERT: E 61 VAL cc_start: 0.8713 (p) cc_final: 0.8479 (p) REVERT: E 63 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8623 (ptpp) REVERT: E 224 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: F 56 TYR cc_start: 0.7509 (p90) cc_final: 0.6900 (p90) REVERT: F 61 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7922 (t) REVERT: F 63 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8345 (ptpp) REVERT: G 164 HIS cc_start: 0.7959 (t-170) cc_final: 0.7575 (t70) REVERT: G 175 HIS cc_start: 0.8956 (m-70) cc_final: 0.8603 (m-70) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 0.1646 time to fit residues: 30.9317 Evaluate side-chains 89 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 135 ARG 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: 0.6980 chunk 194 optimal weight: 0.0050 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 316 GLN B 124 HIS B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046260 restraints weight = 84816.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048072 restraints weight = 41036.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049230 restraints weight = 26344.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049948 restraints weight = 20114.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050414 restraints weight = 17120.499| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20554 Z= 0.160 Angle : 0.625 9.939 28001 Z= 0.318 Chirality : 0.042 0.214 3136 Planarity : 0.005 0.056 3454 Dihedral : 16.703 133.280 3254 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 12.98 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2375 helix: 1.08 (0.14), residues: 1492 sheet: 0.24 (0.38), residues: 196 loop : -0.12 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 327 TYR 0.017 0.001 TYR D 37 PHE 0.023 0.002 PHE B 126 TRP 0.025 0.001 TRP G 267 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (20554) covalent geometry : angle 0.62491 / 0.32 (28001) hydrogen bonds : bond 0.04838 / 3.17 ( 1096) hydrogen bonds : angle 4.27444 / 3.03 ( 2975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9266 (mtm) cc_final: 0.8825 (mtm) REVERT: B 94 ILE cc_start: 0.9101 (tp) cc_final: 0.8809 (tt) REVERT: D 41 MET cc_start: 0.9344 (tpp) cc_final: 0.8768 (tpp) REVERT: D 46 GLU cc_start: 0.8736 (tp30) cc_final: 0.8151 (tp30) REVERT: D 187 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8501 (p0) REVERT: E 25 ASN cc_start: 0.9311 (m-40) cc_final: 0.8939 (m110) REVERT: E 224 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7387 (mtp85) REVERT: E 320 LYS cc_start: 0.9024 (tppt) cc_final: 0.8804 (tppt) REVERT: F 56 TYR cc_start: 0.7513 (p90) cc_final: 0.7086 (p90) REVERT: F 216 ASN cc_start: 0.8837 (m-40) cc_final: 0.8092 (t0) REVERT: G 164 HIS cc_start: 0.7934 (t-170) cc_final: 0.7555 (t-170) REVERT: G 175 HIS cc_start: 0.9030 (m-70) cc_final: 0.8546 (m-70) outliers start: 40 outliers final: 20 residues processed: 119 average time/residue: 0.1217 time to fit residues: 24.3360 Evaluate side-chains 93 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 182 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.067609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046030 restraints weight = 85375.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047825 restraints weight = 41766.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048964 restraints weight = 27018.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049680 restraints weight = 20742.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050134 restraints weight = 17744.609| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20554 Z= 0.144 Angle : 0.569 11.189 28001 Z= 0.287 Chirality : 0.040 0.204 3136 Planarity : 0.004 0.048 3454 Dihedral : 15.406 129.763 3233 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 13.51 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2375 helix: 1.21 (0.14), residues: 1485 sheet: 0.08 (0.38), residues: 196 loop : -0.11 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 215 TYR 0.016 0.001 TYR C 37 PHE 0.013 0.001 PHE A 251 TRP 0.035 0.001 TRP G 267 HIS 0.007 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (20554) covalent geometry : angle 0.56855 / 0.29 (28001) hydrogen bonds : bond 0.04347 / 2.88 ( 1096) hydrogen bonds : angle 4.01493 / 2.83 ( 2975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9174 (mtm) cc_final: 0.8714 (mtm) REVERT: B 94 ILE cc_start: 0.9094 (tp) cc_final: 0.8799 (tt) REVERT: C 286 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9004 (tptp) REVERT: D 41 MET cc_start: 0.9372 (tpp) cc_final: 0.8682 (tpp) REVERT: D 46 GLU cc_start: 0.8758 (tp30) cc_final: 0.8393 (tp30) REVERT: D 187 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8521 (p0) REVERT: E 25 ASN cc_start: 0.9312 (m-40) cc_final: 0.8953 (m-40) REVERT: E 320 LYS cc_start: 0.9044 (tppt) cc_final: 0.8768 (tppt) REVERT: F 56 TYR cc_start: 0.7578 (p90) cc_final: 0.7307 (p90) REVERT: F 216 ASN cc_start: 0.8816 (m-40) cc_final: 0.8085 (t0) REVERT: G 164 HIS cc_start: 0.7988 (t-170) cc_final: 0.7605 (t-170) REVERT: G 175 HIS cc_start: 0.9060 (m-70) cc_final: 0.8562 (m-70) outliers start: 38 outliers final: 26 residues processed: 113 average time/residue: 0.1418 time to fit residues: 26.3670 Evaluate side-chains 98 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 107 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.066782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044952 restraints weight = 85859.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046736 restraints weight = 41836.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047840 restraints weight = 27062.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048568 restraints weight = 20855.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049008 restraints weight = 17815.919| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20554 Z= 0.160 Angle : 0.548 11.559 28001 Z= 0.277 Chirality : 0.040 0.161 3136 Planarity : 0.004 0.046 3454 Dihedral : 14.359 134.086 3229 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.28 % Allowed : 14.00 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2375 helix: 1.31 (0.14), residues: 1486 sheet: -0.08 (0.38), residues: 196 loop : -0.10 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 215 TYR 0.016 0.001 TYR C 37 PHE 0.017 0.001 PHE D 168 TRP 0.039 0.001 TRP G 267 HIS 0.006 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (20554) covalent geometry : angle 0.54767 / 0.28 (28001) hydrogen bonds : bond 0.03915 / 2.61 ( 1096) hydrogen bonds : angle 3.89283 / 2.74 ( 2975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 73 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9144 (mtm) cc_final: 0.8685 (mtm) REVERT: B 94 ILE cc_start: 0.9113 (tp) cc_final: 0.8829 (tt) REVERT: C 286 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9004 (tptp) REVERT: D 41 MET cc_start: 0.9400 (tpp) cc_final: 0.8806 (tpp) REVERT: D 46 GLU cc_start: 0.8795 (tp30) cc_final: 0.8457 (tp30) REVERT: D 187 ASP cc_start: 0.9211 (OUTLIER) cc_final: 0.8519 (p0) REVERT: E 25 ASN cc_start: 0.9336 (m-40) cc_final: 0.8994 (m-40) REVERT: F 216 ASN cc_start: 0.8827 (m-40) cc_final: 0.8065 (t0) REVERT: G 164 HIS cc_start: 0.8158 (t-170) cc_final: 0.7734 (t-170) REVERT: G 175 HIS cc_start: 0.9122 (m-70) cc_final: 0.8529 (m-70) outliers start: 47 outliers final: 30 residues processed: 113 average time/residue: 0.1334 time to fit residues: 25.2487 Evaluate side-chains 102 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS 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 204 CYS Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 254 HIS G 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044990 restraints weight = 85775.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046695 restraints weight = 42906.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047796 restraints weight = 28216.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048482 restraints weight = 21900.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.048907 restraints weight = 18820.905| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20554 Z= 0.151 Angle : 0.527 12.146 28001 Z= 0.266 Chirality : 0.039 0.162 3136 Planarity : 0.004 0.045 3454 Dihedral : 14.120 133.649 3229 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.09 % Allowed : 14.73 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2375 helix: 1.37 (0.14), residues: 1486 sheet: -0.15 (0.38), residues: 196 loop : -0.10 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 223 TYR 0.015 0.001 TYR C 37 PHE 0.011 0.001 PHE E 319 TRP 0.033 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (20554) covalent geometry : angle 0.52733 / 0.27 (28001) hydrogen bonds : bond 0.03807 / 2.54 ( 1096) hydrogen bonds : angle 3.82396 / 2.69 ( 2975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9113 (mtm) cc_final: 0.8639 (mtm) REVERT: B 94 ILE cc_start: 0.9002 (tp) cc_final: 0.8712 (tt) REVERT: C 286 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.8938 (tptp) REVERT: D 41 MET cc_start: 0.9356 (tpp) cc_final: 0.8736 (tpp) REVERT: D 46 GLU cc_start: 0.8799 (tp30) cc_final: 0.8397 (tp30) REVERT: D 187 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8492 (p0) REVERT: E 25 ASN cc_start: 0.9391 (m-40) cc_final: 0.9050 (m-40) REVERT: F 160 LEU cc_start: 0.9489 (tp) cc_final: 0.9254 (tp) REVERT: F 164 HIS cc_start: 0.8934 (t70) cc_final: 0.7949 (t70) REVERT: F 216 ASN cc_start: 0.8856 (m-40) cc_final: 0.8064 (t0) REVERT: G 164 HIS cc_start: 0.8204 (t-170) cc_final: 0.7782 (t-170) REVERT: G 175 HIS cc_start: 0.9143 (m-70) cc_final: 0.8576 (m-70) outliers start: 43 outliers final: 32 residues processed: 110 average time/residue: 0.1240 time to fit residues: 23.5104 Evaluate side-chains 104 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 206 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.044349 restraints weight = 85657.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046022 restraints weight = 43319.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047111 restraints weight = 28633.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047787 restraints weight = 22238.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048190 restraints weight = 19129.750| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20554 Z= 0.175 Angle : 0.547 12.515 28001 Z= 0.275 Chirality : 0.039 0.140 3136 Planarity : 0.004 0.045 3454 Dihedral : 13.966 133.710 3229 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2375 helix: 1.39 (0.14), residues: 1486 sheet: -0.27 (0.37), residues: 196 loop : -0.09 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 223 TYR 0.017 0.001 TYR A 109 PHE 0.015 0.001 PHE E 168 TRP 0.020 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (20554) covalent geometry : angle 0.54711 / 0.27 (28001) hydrogen bonds : bond 0.03830 / 2.58 ( 1096) hydrogen bonds : angle 3.82104 / 2.68 ( 2975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 73 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.9104 (mtm) cc_final: 0.8628 (mtm) REVERT: B 94 ILE cc_start: 0.9069 (tp) cc_final: 0.8794 (tt) REVERT: C 286 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.8965 (tptp) REVERT: D 41 MET cc_start: 0.9382 (tpp) cc_final: 0.8662 (tpp) REVERT: D 46 GLU cc_start: 0.8827 (tp30) cc_final: 0.8454 (tp30) REVERT: D 187 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8501 (p0) REVERT: E 25 ASN cc_start: 0.9394 (m-40) cc_final: 0.9063 (m-40) REVERT: F 160 LEU cc_start: 0.9544 (tp) cc_final: 0.9314 (tp) REVERT: F 164 HIS cc_start: 0.8963 (t70) cc_final: 0.8060 (t70) REVERT: F 216 ASN cc_start: 0.8872 (m-40) cc_final: 0.8025 (t0) REVERT: G 164 HIS cc_start: 0.8295 (t-170) cc_final: 0.7803 (t-170) REVERT: G 175 HIS cc_start: 0.9200 (m-70) cc_final: 0.8634 (m-70) outliers start: 51 outliers final: 37 residues processed: 118 average time/residue: 0.1127 time to fit residues: 22.7051 Evaluate side-chains 108 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 69 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 28 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.067133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045261 restraints weight = 85351.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046986 restraints weight = 42719.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048089 restraints weight = 28083.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048785 restraints weight = 21790.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049203 restraints weight = 18709.059| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20554 Z= 0.111 Angle : 0.504 13.455 28001 Z= 0.254 Chirality : 0.039 0.203 3136 Planarity : 0.004 0.044 3454 Dihedral : 13.807 130.931 3229 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.24 % Allowed : 15.31 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2375 helix: 1.43 (0.14), residues: 1486 sheet: -0.18 (0.38), residues: 196 loop : -0.07 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 215 TYR 0.017 0.001 TYR C 37 PHE 0.010 0.001 PHE C 319 TRP 0.014 0.001 TRP G 267 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20554) covalent geometry : angle 0.50439 / 0.25 (28001) hydrogen bonds : bond 0.03616 / 2.42 ( 1096) hydrogen bonds : angle 3.68795 / 2.58 ( 2975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9553 (t0) cc_final: 0.9111 (t0) REVERT: A 198 MET cc_start: 0.9096 (mtm) cc_final: 0.8640 (mtm) REVERT: B 94 ILE cc_start: 0.8971 (tp) cc_final: 0.8687 (tt) REVERT: C 286 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8901 (tptp) REVERT: D 41 MET cc_start: 0.9316 (tpp) cc_final: 0.8642 (tpp) REVERT: D 46 GLU cc_start: 0.8773 (tp30) cc_final: 0.8374 (tp30) REVERT: D 187 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8494 (p0) REVERT: E 25 ASN cc_start: 0.9410 (m-40) cc_final: 0.9074 (m-40) REVERT: E 198 MET cc_start: 0.9076 (ttp) cc_final: 0.8830 (ttp) REVERT: F 69 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8589 (tmm-80) REVERT: F 160 LEU cc_start: 0.9539 (tp) cc_final: 0.9321 (tp) REVERT: F 164 HIS cc_start: 0.8959 (t70) cc_final: 0.8102 (t70) REVERT: F 216 ASN cc_start: 0.8896 (m-40) cc_final: 0.8038 (t0) REVERT: G 164 HIS cc_start: 0.8268 (t-170) cc_final: 0.7770 (t-170) REVERT: G 175 HIS cc_start: 0.9203 (m-70) cc_final: 0.8653 (m-70) outliers start: 46 outliers final: 27 residues processed: 121 average time/residue: 0.1077 time to fit residues: 22.1508 Evaluate side-chains 102 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 190 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044665 restraints weight = 85776.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046362 restraints weight = 43356.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047450 restraints weight = 28576.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048138 restraints weight = 22199.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048548 restraints weight = 19079.178| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20554 Z= 0.154 Angle : 0.533 13.909 28001 Z= 0.266 Chirality : 0.039 0.200 3136 Planarity : 0.004 0.044 3454 Dihedral : 13.780 130.964 3229 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 15.95 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2375 helix: 1.45 (0.14), residues: 1486 sheet: -0.24 (0.38), residues: 196 loop : -0.08 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 224 TYR 0.015 0.001 TYR C 37 PHE 0.010 0.001 PHE C 168 TRP 0.011 0.001 TRP G 267 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (20554) covalent geometry : angle 0.53327 / 0.27 (28001) hydrogen bonds : bond 0.03645 / 2.44 ( 1096) hydrogen bonds : angle 3.71744 / 2.60 ( 2975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9548 (t0) cc_final: 0.9113 (t0) REVERT: B 94 ILE cc_start: 0.9010 (tp) cc_final: 0.8727 (tt) REVERT: C 286 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8907 (tptp) REVERT: D 41 MET cc_start: 0.9335 (tpp) cc_final: 0.8638 (tpp) REVERT: D 46 GLU cc_start: 0.8812 (tp30) cc_final: 0.8438 (tp30) REVERT: D 187 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.8506 (p0) REVERT: E 25 ASN cc_start: 0.9412 (m-40) cc_final: 0.9081 (m-40) REVERT: E 198 MET cc_start: 0.9064 (ttp) cc_final: 0.8829 (ttp) REVERT: F 69 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8587 (tmm-80) REVERT: F 160 LEU cc_start: 0.9554 (tp) cc_final: 0.9334 (tp) REVERT: F 164 HIS cc_start: 0.8969 (t70) cc_final: 0.8135 (t70) REVERT: F 216 ASN cc_start: 0.8902 (m-40) cc_final: 0.8094 (t0) REVERT: G 164 HIS cc_start: 0.8310 (t-170) cc_final: 0.7819 (t-170) REVERT: G 175 HIS cc_start: 0.9202 (m-70) cc_final: 0.8655 (m-70) outliers start: 40 outliers final: 32 residues processed: 106 average time/residue: 0.1142 time to fit residues: 20.3422 Evaluate side-chains 105 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 228 optimal weight: 0.0270 chunk 81 optimal weight: 0.3980 chunk 216 optimal weight: 7.9990 chunk 225 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045646 restraints weight = 84901.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047369 restraints weight = 42498.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048480 restraints weight = 27897.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049155 restraints weight = 21629.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.049588 restraints weight = 18602.975| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20554 Z= 0.101 Angle : 0.504 13.863 28001 Z= 0.252 Chirality : 0.038 0.187 3136 Planarity : 0.003 0.044 3454 Dihedral : 13.646 127.684 3229 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.65 % Allowed : 16.29 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2375 helix: 1.45 (0.14), residues: 1486 sheet: -0.18 (0.38), residues: 196 loop : -0.07 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.015 0.001 TYR C 37 PHE 0.012 0.001 PHE C 319 TRP 0.011 0.001 TRP G 267 HIS 0.003 0.001 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (20554) covalent geometry : angle 0.50381 / 0.25 (28001) hydrogen bonds : bond 0.03446 / 2.30 ( 1096) hydrogen bonds : angle 3.60554 / 2.52 ( 2975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9559 (t0) cc_final: 0.9125 (t0) REVERT: A 198 MET cc_start: 0.8995 (mtm) cc_final: 0.8583 (mtm) REVERT: B 94 ILE cc_start: 0.8975 (tp) cc_final: 0.8686 (tt) REVERT: C 286 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9184 (tttt) REVERT: D 41 MET cc_start: 0.9289 (tpp) cc_final: 0.8649 (tpp) REVERT: D 46 GLU cc_start: 0.8754 (tp30) cc_final: 0.8401 (tp30) REVERT: D 187 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8481 (p0) REVERT: E 25 ASN cc_start: 0.9414 (m-40) cc_final: 0.9087 (m110) REVERT: E 198 MET cc_start: 0.9013 (ttp) cc_final: 0.8812 (ttp) REVERT: F 69 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8600 (tmm-80) REVERT: F 160 LEU cc_start: 0.9553 (tp) cc_final: 0.9339 (tp) REVERT: F 164 HIS cc_start: 0.8956 (t70) cc_final: 0.8193 (t70) REVERT: F 216 ASN cc_start: 0.8906 (m-40) cc_final: 0.8098 (t0) REVERT: G 164 HIS cc_start: 0.8346 (t-170) cc_final: 0.7854 (t-170) REVERT: G 175 HIS cc_start: 0.9206 (m-70) cc_final: 0.8751 (m-70) outliers start: 34 outliers final: 28 residues processed: 106 average time/residue: 0.1304 time to fit residues: 22.9710 Evaluate side-chains 100 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 186 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 157 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.045092 restraints weight = 85662.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046803 restraints weight = 43131.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047905 restraints weight = 28427.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048577 restraints weight = 22047.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049016 restraints weight = 18980.766| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20554 Z= 0.131 Angle : 0.515 13.436 28001 Z= 0.257 Chirality : 0.039 0.171 3136 Planarity : 0.003 0.043 3454 Dihedral : 13.612 127.451 3229 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.60 % Allowed : 16.43 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2375 helix: 1.49 (0.14), residues: 1486 sheet: -0.19 (0.38), residues: 196 loop : -0.05 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.013 0.001 TYR C 37 PHE 0.009 0.001 PHE D 214 TRP 0.010 0.001 TRP G 267 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (20554) covalent geometry : angle 0.51457 / 0.26 (28001) hydrogen bonds : bond 0.03476 / 2.33 ( 1096) hydrogen bonds : angle 3.61893 / 2.52 ( 2975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.9564 (t0) cc_final: 0.9131 (t0) REVERT: A 198 MET cc_start: 0.8979 (mtm) cc_final: 0.8569 (mtm) REVERT: B 94 ILE cc_start: 0.9055 (tp) cc_final: 0.8773 (tt) REVERT: C 286 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9217 (tttt) REVERT: D 41 MET cc_start: 0.9344 (tpp) cc_final: 0.8698 (tpp) REVERT: D 46 GLU cc_start: 0.8796 (tp30) cc_final: 0.8455 (tp30) REVERT: D 187 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8471 (p0) REVERT: E 25 ASN cc_start: 0.9400 (m-40) cc_final: 0.9074 (m-40) REVERT: E 198 MET cc_start: 0.9020 (ttp) cc_final: 0.8817 (ttp) REVERT: F 69 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8607 (tmm-80) REVERT: F 160 LEU cc_start: 0.9572 (tp) cc_final: 0.9351 (tp) REVERT: F 164 HIS cc_start: 0.8959 (t70) cc_final: 0.8270 (t-90) REVERT: F 216 ASN cc_start: 0.8904 (m-40) cc_final: 0.8099 (t0) REVERT: G 164 HIS cc_start: 0.8395 (t-170) cc_final: 0.7896 (t-170) REVERT: G 175 HIS cc_start: 0.9226 (m-70) cc_final: 0.8766 (m-70) outliers start: 33 outliers final: 29 residues processed: 100 average time/residue: 0.1335 time to fit residues: 22.5481 Evaluate side-chains 100 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 307 LYS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 146 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044245 restraints weight = 86173.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045807 restraints weight = 45970.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046815 restraints weight = 31424.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047441 restraints weight = 25035.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047793 restraints weight = 21854.849| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20554 Z= 0.209 Angle : 0.590 12.723 28001 Z= 0.293 Chirality : 0.040 0.164 3136 Planarity : 0.004 0.043 3454 Dihedral : 13.677 127.778 3229 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.75 % Allowed : 16.24 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2375 helix: 1.48 (0.14), residues: 1486 sheet: -0.39 (0.37), residues: 196 loop : -0.05 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 14 TYR 0.015 0.001 TYR F 56 PHE 0.013 0.001 PHE C 168 TRP 0.011 0.001 TRP C 284 HIS 0.005 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (20554) covalent geometry : angle 0.59039 / 0.29 (28001) hydrogen bonds : bond 0.03836 / 2.59 ( 1096) hydrogen bonds : angle 3.80870 / 2.66 ( 2975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.35 seconds wall clock time: 61 minutes 15.07 seconds (3675.07 seconds total)