Starting phenix.real_space_refine on Mon Apr 6 06:01:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7o_72313/04_2026/9q7o_72313.map" } resolution = 3.02 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= 0.001 sd= 0.005 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 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 10061 2.51 5 N 2682 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15919 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2821 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1358 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.50, per 1000 atoms: 0.22 Number of scatterers: 15919 At special positions: 0 Unit cell: (81.972, 99.36, 212.796, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 3053 8.00 N 2682 7.00 C 10061 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: 1.10 Conformation dependent library (CDL) restraints added in 671.9 milliseconds 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 50.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.551A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.914A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.885A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.333A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.797A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.796A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.513A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.674A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.598A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.520A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.789A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.754A pdb=" N LEU B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.832A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.753A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.714A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.508A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.624A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.537A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.514A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.101A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.795A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.663A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.692A pdb=" N ILE C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.592A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.502A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.619A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.569A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.523A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.121A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.646A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.694A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.618A pdb=" N ILE D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.606A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.523A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.654A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.127A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.570A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.204A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.511A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.651A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.663A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.643A pdb=" N ILE E 289 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.633A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.642A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.117A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 66 Processing helix chain 'W' and resid 67 through 80 Processing helix chain 'W' and resid 81 through 107 removed outlier: 3.529A pdb=" N LYS W 85 " --> pdb=" O GLY W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 136 Proline residue: W 121 - end of helix removed outlier: 3.594A pdb=" N ASN W 136 " --> pdb=" O PHE W 132 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 150 Processing helix chain 'W' and resid 151 through 158 removed outlier: 3.500A pdb=" N ALA W 154 " --> pdb=" O SER W 151 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL W 158 " --> pdb=" O LEU W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 187 removed outlier: 4.083A pdb=" N TYR W 167 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR W 178 " --> pdb=" O ALA W 174 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG W 181 " --> pdb=" O PHE W 177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS W 187 " --> pdb=" O LEU W 183 " (cutoff:3.500A) Processing helix chain 'W' and resid 190 through 215 removed outlier: 4.175A pdb=" N VAL W 194 " --> pdb=" O ASP W 190 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP W 204 " --> pdb=" O TYR W 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.682A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.802A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 removed outlier: 4.157A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.385A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.905A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.392A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.857A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.633A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 250 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.740A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.034A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.772A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.758A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.030A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.087A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.086A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 764 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4348 1.34 - 1.46: 2957 1.46 - 1.57: 8758 1.57 - 1.69: 15 1.69 - 1.81: 190 Bond restraints: 16268 Sorted by residual: bond pdb=" C LEU A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.335 1.398 -0.064 1.28e-02 6.10e+03 2.48e+01 bond pdb=" CA GLU A 241 " pdb=" CB GLU A 241 " ideal model delta sigma weight residual 1.525 1.570 -0.045 1.29e-02 6.01e+03 1.20e+01 bond pdb=" C ALA W 161 " pdb=" N PRO W 162 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.77e+00 bond pdb=" C GLN A 263 " pdb=" N PRO A 264 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.25e-02 6.40e+03 5.74e+00 bond pdb=" C ALA W 120 " pdb=" N PRO W 121 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.23e-02 6.61e+03 5.40e+00 ... (remaining 16263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 21280 2.59 - 5.19: 662 5.19 - 7.78: 108 7.78 - 10.37: 25 10.37 - 12.96: 2 Bond angle restraints: 22077 Sorted by residual: angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 122.08 131.15 -9.07 1.47e+00 4.63e-01 3.81e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 122.08 130.51 -8.43 1.47e+00 4.63e-01 3.29e+01 angle pdb=" C THR A 202 " pdb=" N THR A 203 " pdb=" CA THR A 203 " ideal model delta sigma weight residual 120.38 128.50 -8.12 1.46e+00 4.69e-01 3.09e+01 angle pdb=" N THR A 203 " pdb=" CA THR A 203 " pdb=" C THR A 203 " ideal model delta sigma weight residual 111.75 118.13 -6.38 1.28e+00 6.10e-01 2.48e+01 angle pdb=" C GLU A 253 " pdb=" N ARG A 254 " pdb=" CA ARG A 254 " ideal model delta sigma weight residual 120.79 127.64 -6.85 1.39e+00 5.18e-01 2.43e+01 ... (remaining 22072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 9687 35.86 - 71.72: 84 71.72 - 107.59: 11 107.59 - 143.45: 0 143.45 - 179.31: 2 Dihedral angle restraints: 9784 sinusoidal: 3948 harmonic: 5836 Sorted by residual: dihedral pdb=" CA ALA W 161 " pdb=" C ALA W 161 " pdb=" N PRO W 162 " pdb=" CA PRO W 162 " ideal model delta harmonic sigma weight residual -180.00 -112.26 -67.74 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA VAL A 201 " pdb=" C VAL A 201 " pdb=" N THR A 202 " pdb=" CA THR A 202 " ideal model delta harmonic sigma weight residual 180.00 127.08 52.92 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 120.69 179.31 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2239 0.102 - 0.203: 186 0.203 - 0.305: 25 0.305 - 0.407: 3 0.407 - 0.508: 1 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE B 287 " pdb=" CA ILE B 287 " pdb=" CG1 ILE B 287 " pdb=" CG2 ILE B 287 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2451 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA W 55 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO W 56 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO W 56 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO W 56 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO B 164 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 164 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.044 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 63 2.68 - 3.23: 13593 3.23 - 3.79: 24315 3.79 - 4.34: 34100 4.34 - 4.90: 55840 Nonbonded interactions: 127911 Sorted by model distance: nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.121 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.135 2.170 nonbonded pdb=" O2B ADP A 400 " pdb="MG MG A 401 " model vdw 2.154 2.170 nonbonded pdb=" O2B ADP B 400 " pdb="MG MG B 401 " model vdw 2.166 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.197 2.170 ... (remaining 127906 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 'A' and (resid 5 through 39 or resid 51 through 401)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 39 or resid 51 through 401)) selection = (chain 'D' and (resid 5 through 39 or resid 51 through 401)) selection = (chain 'E' and (resid 5 through 39 or resid 51 through 401)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.073 16268 Z= 0.270 Angle : 1.070 12.965 22077 Z= 0.581 Chirality : 0.061 0.508 2454 Planarity : 0.009 0.091 2816 Dihedral : 11.986 179.309 6044 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.05 % 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: -2.55 (0.17), residues: 1987 helix: -2.58 (0.12), residues: 866 sheet: -0.10 (0.29), residues: 326 loop : -1.06 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 37 TYR 0.039 0.002 TYR E 143 PHE 0.022 0.003 PHE D 124 TRP 0.021 0.002 TRP W 204 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00524 (16268) covalent geometry : angle 1.06994 (22077) hydrogen bonds : bond 0.14887 ( 756) hydrogen bonds : angle 6.95561 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9159 (tpp) cc_final: 0.8908 (mmm) REVERT: B 118 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8431 (mmtm) REVERT: C 305 MET cc_start: 0.9330 (mmm) cc_final: 0.9023 (mmm) REVERT: E 82 MET cc_start: 0.9061 (tpt) cc_final: 0.8860 (tpt) REVERT: E 283 MET cc_start: 0.9154 (mmm) cc_final: 0.8541 (mmm) REVERT: E 355 MET cc_start: 0.9171 (mtp) cc_final: 0.8919 (mmm) REVERT: W 61 PHE cc_start: 0.9454 (t80) cc_final: 0.9183 (t80) REVERT: W 89 MET cc_start: 0.9218 (mtt) cc_final: 0.9013 (mtp) REVERT: W 132 PHE cc_start: 0.9283 (t80) cc_final: 0.8794 (t80) REVERT: W 166 PRO cc_start: 0.9377 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: W 169 LYS cc_start: 0.9460 (tttt) cc_final: 0.9216 (ttpp) REVERT: W 196 TRP cc_start: 0.9645 (t60) cc_final: 0.9131 (t60) REVERT: W 204 TRP cc_start: 0.8916 (m100) cc_final: 0.8402 (m100) REVERT: W 215 HIS cc_start: 0.8288 (m-70) cc_final: 0.7454 (m170) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1417 time to fit residues: 39.3784 Evaluate side-chains 138 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.0060 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS E 371 HIS W 144 HIS W 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.057052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043805 restraints weight = 68646.284| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.31 r_work: 0.2869 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16268 Z= 0.112 Angle : 0.596 6.718 22077 Z= 0.293 Chirality : 0.043 0.153 2454 Planarity : 0.005 0.053 2816 Dihedral : 7.635 170.950 2255 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.05 % 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: -0.66 (0.19), residues: 1987 helix: -0.51 (0.16), residues: 881 sheet: 0.16 (0.29), residues: 348 loop : -0.39 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.017 0.001 TYR W 72 PHE 0.014 0.001 PHE B 127 TRP 0.011 0.001 TRP B 86 HIS 0.006 0.001 HIS W 193 Details of bonding type rmsd covalent geometry : bond 0.00253 (16268) covalent geometry : angle 0.59566 (22077) hydrogen bonds : bond 0.02954 ( 756) hydrogen bonds : angle 4.89101 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9299 (mmp) cc_final: 0.9040 (mmt) REVERT: A 227 MET cc_start: 0.8940 (mmm) cc_final: 0.8721 (mmm) REVERT: A 355 MET cc_start: 0.9147 (mmm) cc_final: 0.8649 (mpp) REVERT: B 118 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8543 (mmmt) REVERT: C 44 MET cc_start: 0.7860 (mmm) cc_final: 0.7487 (mmt) REVERT: E 355 MET cc_start: 0.9213 (mtp) cc_final: 0.8923 (mmm) REVERT: W 59 GLN cc_start: 0.9323 (mt0) cc_final: 0.9085 (mp10) REVERT: W 61 PHE cc_start: 0.9487 (t80) cc_final: 0.9237 (t80) REVERT: W 89 MET cc_start: 0.9301 (mtt) cc_final: 0.9096 (mtp) REVERT: W 100 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9274 (mt) REVERT: W 132 PHE cc_start: 0.9340 (t80) cc_final: 0.8725 (t80) REVERT: W 136 ASN cc_start: 0.8744 (m-40) cc_final: 0.8226 (m110) REVERT: W 166 PRO cc_start: 0.9459 (Cg_exo) cc_final: 0.9014 (Cg_endo) REVERT: W 176 MET cc_start: 0.9086 (mmm) cc_final: 0.8716 (tpt) REVERT: W 193 HIS cc_start: 0.9051 (m90) cc_final: 0.8600 (m90) REVERT: W 196 TRP cc_start: 0.9557 (t60) cc_final: 0.9144 (t60) REVERT: W 200 TYR cc_start: 0.8996 (t80) cc_final: 0.8723 (t80) REVERT: W 215 HIS cc_start: 0.8198 (m-70) cc_final: 0.7812 (m170) outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.1202 time to fit residues: 27.1668 Evaluate side-chains 140 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 188 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 39 optimal weight: 0.0070 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS W 172 ASN W 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039485 restraints weight = 70133.835| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.21 r_work: 0.2738 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16268 Z= 0.242 Angle : 0.659 6.439 22077 Z= 0.327 Chirality : 0.047 0.176 2454 Planarity : 0.004 0.047 2816 Dihedral : 7.840 170.318 2255 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.47 % Allowed : 4.47 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.02 (0.20), residues: 1987 helix: 0.24 (0.17), residues: 902 sheet: 0.22 (0.29), residues: 354 loop : -0.23 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 256 TYR 0.014 0.001 TYR W 57 PHE 0.013 0.002 PHE B 223 TRP 0.039 0.002 TRP W 221 HIS 0.010 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00563 (16268) covalent geometry : angle 0.65881 (22077) hydrogen bonds : bond 0.03524 ( 756) hydrogen bonds : angle 4.67254 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 355 MET cc_start: 0.9155 (mmm) cc_final: 0.8623 (mmm) REVERT: B 118 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8584 (mmmt) REVERT: B 360 GLN cc_start: 0.8957 (mp10) cc_final: 0.8537 (pm20) REVERT: C 44 MET cc_start: 0.7914 (mmm) cc_final: 0.7360 (mmt) REVERT: E 355 MET cc_start: 0.9204 (mtp) cc_final: 0.8927 (mmm) REVERT: W 59 GLN cc_start: 0.9225 (mt0) cc_final: 0.8954 (mp10) REVERT: W 61 PHE cc_start: 0.9466 (t80) cc_final: 0.9155 (t80) REVERT: W 89 MET cc_start: 0.9309 (mtt) cc_final: 0.9058 (mtp) REVERT: W 132 PHE cc_start: 0.9313 (t80) cc_final: 0.8738 (t80) REVERT: W 136 ASN cc_start: 0.8912 (m-40) cc_final: 0.8357 (m110) REVERT: W 137 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7286 (mtp85) REVERT: W 142 PHE cc_start: 0.8572 (t80) cc_final: 0.8250 (t80) REVERT: W 176 MET cc_start: 0.9175 (mmm) cc_final: 0.8841 (tpt) REVERT: W 193 HIS cc_start: 0.9152 (m90) cc_final: 0.8920 (m-70) REVERT: W 196 TRP cc_start: 0.9570 (t60) cc_final: 0.9076 (t60) outliers start: 8 outliers final: 5 residues processed: 140 average time/residue: 0.1104 time to fit residues: 24.0174 Evaluate side-chains 136 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 160 MET Chi-restraints excluded: chain W residue 211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 0.0370 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 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 = 0.3345 r_free = 0.3345 target = 0.053557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040482 restraints weight = 69083.157| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.18 r_work: 0.2773 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16268 Z= 0.110 Angle : 0.559 7.245 22077 Z= 0.269 Chirality : 0.043 0.168 2454 Planarity : 0.004 0.057 2816 Dihedral : 7.489 173.186 2255 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.47 % Allowed : 5.29 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.39 (0.20), residues: 1987 helix: 0.65 (0.18), residues: 898 sheet: 0.32 (0.29), residues: 346 loop : -0.06 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 133 TYR 0.026 0.001 TYR W 210 PHE 0.008 0.001 PHE C 124 TRP 0.015 0.001 TRP W 221 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00254 (16268) covalent geometry : angle 0.55888 (22077) hydrogen bonds : bond 0.02690 ( 756) hydrogen bonds : angle 4.45174 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9392 (mmm) cc_final: 0.8641 (mmm) REVERT: A 355 MET cc_start: 0.9123 (mmm) cc_final: 0.8528 (mpp) REVERT: B 118 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8558 (mmmt) REVERT: B 360 GLN cc_start: 0.8966 (mp10) cc_final: 0.8552 (pm20) REVERT: C 44 MET cc_start: 0.7780 (mmm) cc_final: 0.7430 (mmt) REVERT: C 269 MET cc_start: 0.9032 (mtp) cc_final: 0.8825 (mtp) REVERT: E 44 MET cc_start: 0.8358 (mtt) cc_final: 0.8121 (mmm) REVERT: E 355 MET cc_start: 0.9161 (mtp) cc_final: 0.8907 (mmm) REVERT: W 59 GLN cc_start: 0.9233 (mt0) cc_final: 0.8948 (mp10) REVERT: W 61 PHE cc_start: 0.9466 (t80) cc_final: 0.9161 (t80) REVERT: W 89 MET cc_start: 0.9312 (mtt) cc_final: 0.9072 (mtp) REVERT: W 108 GLN cc_start: 0.8107 (pp30) cc_final: 0.7859 (pp30) REVERT: W 132 PHE cc_start: 0.9285 (t80) cc_final: 0.8721 (t80) REVERT: W 136 ASN cc_start: 0.8875 (m-40) cc_final: 0.8392 (m110) REVERT: W 142 PHE cc_start: 0.8516 (t80) cc_final: 0.8231 (t80) REVERT: W 176 MET cc_start: 0.9181 (mmm) cc_final: 0.8845 (tpt) REVERT: W 193 HIS cc_start: 0.9099 (m90) cc_final: 0.8558 (m90) REVERT: W 196 TRP cc_start: 0.9556 (t60) cc_final: 0.9035 (t60) REVERT: W 200 TYR cc_start: 0.9228 (t80) cc_final: 0.8942 (t80) outliers start: 8 outliers final: 3 residues processed: 139 average time/residue: 0.1145 time to fit residues: 24.9529 Evaluate side-chains 134 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 160 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 42 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.053076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039927 restraints weight = 69157.730| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.17 r_work: 0.2757 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16268 Z= 0.140 Angle : 0.567 7.605 22077 Z= 0.274 Chirality : 0.044 0.189 2454 Planarity : 0.003 0.056 2816 Dihedral : 7.431 173.939 2255 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.59 % Allowed : 5.70 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.60 (0.20), residues: 1987 helix: 0.85 (0.18), residues: 898 sheet: 0.34 (0.29), residues: 348 loop : 0.06 (0.25), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 133 TYR 0.012 0.001 TYR W 210 PHE 0.010 0.001 PHE D 124 TRP 0.015 0.001 TRP B 86 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00326 (16268) covalent geometry : angle 0.56675 (22077) hydrogen bonds : bond 0.02809 ( 756) hydrogen bonds : angle 4.38640 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9378 (mmm) cc_final: 0.8524 (mmm) REVERT: A 355 MET cc_start: 0.9143 (mmm) cc_final: 0.8544 (mpp) REVERT: B 118 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8580 (mmmt) REVERT: B 360 GLN cc_start: 0.9024 (mp10) cc_final: 0.8643 (pm20) REVERT: C 44 MET cc_start: 0.7734 (mmm) cc_final: 0.7507 (mmt) REVERT: E 44 MET cc_start: 0.8451 (mtt) cc_final: 0.8212 (mmm) REVERT: E 355 MET cc_start: 0.9154 (mtp) cc_final: 0.8907 (mmm) REVERT: W 59 GLN cc_start: 0.9225 (mt0) cc_final: 0.8909 (mp10) REVERT: W 61 PHE cc_start: 0.9454 (t80) cc_final: 0.9153 (t80) REVERT: W 84 GLN cc_start: 0.9385 (pt0) cc_final: 0.9162 (mp10) REVERT: W 89 MET cc_start: 0.9291 (mtt) cc_final: 0.9038 (mtp) REVERT: W 132 PHE cc_start: 0.9275 (t80) cc_final: 0.8692 (t80) REVERT: W 136 ASN cc_start: 0.8846 (m-40) cc_final: 0.8333 (m110) REVERT: W 137 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7412 (mtp180) REVERT: W 142 PHE cc_start: 0.8565 (t80) cc_final: 0.8298 (t80) REVERT: W 176 MET cc_start: 0.9210 (mmm) cc_final: 0.8875 (tpt) REVERT: W 193 HIS cc_start: 0.9115 (m90) cc_final: 0.8906 (m-70) REVERT: W 196 TRP cc_start: 0.9577 (t60) cc_final: 0.9047 (t60) outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.1123 time to fit residues: 24.5009 Evaluate side-chains 134 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 160 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040196 restraints weight = 68853.934| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.17 r_work: 0.2765 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16268 Z= 0.111 Angle : 0.555 7.500 22077 Z= 0.265 Chirality : 0.043 0.200 2454 Planarity : 0.003 0.062 2816 Dihedral : 7.323 175.298 2255 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.53 % Allowed : 5.64 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.74 (0.20), residues: 1987 helix: 0.97 (0.18), residues: 899 sheet: 0.39 (0.29), residues: 346 loop : 0.13 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 133 TYR 0.026 0.001 TYR W 210 PHE 0.008 0.001 PHE D 124 TRP 0.016 0.001 TRP B 86 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00259 (16268) covalent geometry : angle 0.55478 (22077) hydrogen bonds : bond 0.02607 ( 756) hydrogen bonds : angle 4.28961 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9350 (mmm) cc_final: 0.8576 (mmm) REVERT: A 355 MET cc_start: 0.9152 (mmm) cc_final: 0.8571 (mpp) REVERT: B 118 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8549 (mmmt) REVERT: B 360 GLN cc_start: 0.9033 (mp10) cc_final: 0.8665 (pm20) REVERT: C 44 MET cc_start: 0.7783 (mmm) cc_final: 0.7537 (mmt) REVERT: E 44 MET cc_start: 0.8431 (mtt) cc_final: 0.8182 (mmm) REVERT: E 355 MET cc_start: 0.9123 (mtp) cc_final: 0.8886 (mmm) REVERT: W 59 GLN cc_start: 0.9206 (mt0) cc_final: 0.8898 (mp10) REVERT: W 61 PHE cc_start: 0.9435 (t80) cc_final: 0.9133 (t80) REVERT: W 84 GLN cc_start: 0.9372 (pt0) cc_final: 0.9152 (mp10) REVERT: W 89 MET cc_start: 0.9267 (mtt) cc_final: 0.9004 (mtp) REVERT: W 108 GLN cc_start: 0.8217 (pp30) cc_final: 0.7408 (mt0) REVERT: W 132 PHE cc_start: 0.9259 (t80) cc_final: 0.8635 (t80) REVERT: W 136 ASN cc_start: 0.8910 (m-40) cc_final: 0.8386 (m110) REVERT: W 137 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7325 (mtp180) REVERT: W 142 PHE cc_start: 0.8583 (t80) cc_final: 0.8319 (t80) REVERT: W 176 MET cc_start: 0.9200 (mmm) cc_final: 0.8857 (tpt) REVERT: W 196 TRP cc_start: 0.9565 (t60) cc_final: 0.9037 (t60) outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.1114 time to fit residues: 23.6120 Evaluate side-chains 134 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 160 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 124 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** W 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.052074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039073 restraints weight = 68896.099| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.10 r_work: 0.2721 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16268 Z= 0.205 Angle : 0.609 8.259 22077 Z= 0.295 Chirality : 0.046 0.219 2454 Planarity : 0.004 0.060 2816 Dihedral : 7.584 177.627 2255 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.76 % Allowed : 5.94 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.67 (0.20), residues: 1987 helix: 0.92 (0.18), residues: 903 sheet: 0.25 (0.29), residues: 346 loop : 0.13 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.012 0.001 TYR W 200 PHE 0.009 0.001 PHE E 124 TRP 0.010 0.001 TRP B 86 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00479 (16268) covalent geometry : angle 0.60923 (22077) hydrogen bonds : bond 0.03047 ( 756) hydrogen bonds : angle 4.37266 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9395 (mmm) cc_final: 0.8612 (mmm) REVERT: A 355 MET cc_start: 0.9159 (mmm) cc_final: 0.8536 (mpp) REVERT: B 72 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8028 (pp20) REVERT: B 118 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8610 (mmmt) REVERT: B 360 GLN cc_start: 0.9030 (mp10) cc_final: 0.8734 (pm20) REVERT: E 305 MET cc_start: 0.9428 (mmm) cc_final: 0.9210 (mmm) REVERT: E 355 MET cc_start: 0.9161 (mtp) cc_final: 0.8933 (mmm) REVERT: W 59 GLN cc_start: 0.9194 (mt0) cc_final: 0.8874 (mp10) REVERT: W 61 PHE cc_start: 0.9424 (t80) cc_final: 0.9121 (t80) REVERT: W 89 MET cc_start: 0.9245 (mtt) cc_final: 0.8959 (mtp) REVERT: W 108 GLN cc_start: 0.8368 (pp30) cc_final: 0.7592 (mt0) REVERT: W 132 PHE cc_start: 0.9246 (t80) cc_final: 0.8658 (t80) REVERT: W 136 ASN cc_start: 0.8907 (m-40) cc_final: 0.8383 (m110) REVERT: W 137 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7390 (mtp180) REVERT: W 142 PHE cc_start: 0.8673 (t80) cc_final: 0.8437 (t80) REVERT: W 176 MET cc_start: 0.9213 (mmm) cc_final: 0.8847 (tpt) REVERT: W 196 TRP cc_start: 0.9561 (t60) cc_final: 0.9109 (t60) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.1091 time to fit residues: 24.0580 Evaluate side-chains 138 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 160 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN W 84 GLN ** W 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040160 restraints weight = 68735.813| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.10 r_work: 0.2759 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16268 Z= 0.103 Angle : 0.553 8.104 22077 Z= 0.264 Chirality : 0.043 0.205 2454 Planarity : 0.003 0.052 2816 Dihedral : 7.373 178.589 2255 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.89 (0.20), residues: 1987 helix: 1.09 (0.18), residues: 899 sheet: 0.31 (0.29), residues: 346 loop : 0.31 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 133 TYR 0.027 0.001 TYR W 210 PHE 0.007 0.001 PHE D 255 TRP 0.012 0.001 TRP B 86 HIS 0.006 0.001 HIS W 193 Details of bonding type rmsd covalent geometry : bond 0.00239 (16268) covalent geometry : angle 0.55298 (22077) hydrogen bonds : bond 0.02561 ( 756) hydrogen bonds : angle 4.22445 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9343 (mmm) cc_final: 0.8628 (mmm) REVERT: A 355 MET cc_start: 0.9139 (mmm) cc_final: 0.8895 (mmp) REVERT: B 72 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8001 (pp20) REVERT: B 118 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8597 (mmmt) REVERT: B 360 GLN cc_start: 0.9047 (mp10) cc_final: 0.8735 (pm20) REVERT: E 355 MET cc_start: 0.9123 (mtp) cc_final: 0.8902 (mmm) REVERT: W 57 TYR cc_start: 0.8813 (p90) cc_final: 0.8450 (p90) REVERT: W 59 GLN cc_start: 0.9187 (mt0) cc_final: 0.8872 (mp10) REVERT: W 61 PHE cc_start: 0.9429 (t80) cc_final: 0.9124 (t80) REVERT: W 89 MET cc_start: 0.9229 (mtt) cc_final: 0.8940 (mtp) REVERT: W 108 GLN cc_start: 0.8440 (pp30) cc_final: 0.7717 (mt0) REVERT: W 132 PHE cc_start: 0.9226 (t80) cc_final: 0.8624 (t80) REVERT: W 136 ASN cc_start: 0.8898 (m-40) cc_final: 0.8386 (m110) REVERT: W 137 ARG cc_start: 0.7494 (mtp85) cc_final: 0.7216 (mtp180) REVERT: W 142 PHE cc_start: 0.8670 (t80) cc_final: 0.8432 (t80) REVERT: W 176 MET cc_start: 0.9203 (mmm) cc_final: 0.8850 (tpt) REVERT: W 196 TRP cc_start: 0.9601 (t60) cc_final: 0.9129 (t60) outliers start: 9 outliers final: 6 residues processed: 140 average time/residue: 0.1067 time to fit residues: 23.7828 Evaluate side-chains 137 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain W residue 86 HIS Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 160 MET Chi-restraints excluded: chain W residue 211 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 162 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 179 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 GLN ** W 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039616 restraints weight = 68501.650| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.14 r_work: 0.2746 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16268 Z= 0.134 Angle : 0.569 8.663 22077 Z= 0.273 Chirality : 0.044 0.222 2454 Planarity : 0.003 0.051 2816 Dihedral : 7.375 178.596 2255 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.53 % Allowed : 6.53 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.85 (0.20), residues: 1987 helix: 1.09 (0.18), residues: 904 sheet: 0.30 (0.29), residues: 346 loop : 0.21 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.012 0.001 TYR W 200 PHE 0.012 0.001 PHE D 124 TRP 0.018 0.001 TRP B 86 HIS 0.007 0.001 HIS W 193 Details of bonding type rmsd covalent geometry : bond 0.00314 (16268) covalent geometry : angle 0.56931 (22077) hydrogen bonds : bond 0.02682 ( 756) hydrogen bonds : angle 4.22827 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 355 MET cc_start: 0.9160 (mmm) cc_final: 0.8931 (mmp) REVERT: B 62 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7458 (ptp-110) REVERT: B 72 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8071 (pp20) REVERT: B 118 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8583 (mmmt) REVERT: B 360 GLN cc_start: 0.9041 (mp10) cc_final: 0.8728 (pm20) REVERT: C 47 MET cc_start: 0.7238 (pmm) cc_final: 0.6940 (pmm) REVERT: E 44 MET cc_start: 0.8715 (mtt) cc_final: 0.8374 (mtt) REVERT: E 47 MET cc_start: 0.7519 (pmm) cc_final: 0.7134 (pmm) REVERT: E 305 MET cc_start: 0.9413 (mmm) cc_final: 0.9188 (mmm) REVERT: E 355 MET cc_start: 0.9112 (mtp) cc_final: 0.8888 (mmm) REVERT: W 57 TYR cc_start: 0.8828 (p90) cc_final: 0.8525 (p90) REVERT: W 59 GLN cc_start: 0.9176 (mt0) cc_final: 0.8863 (mp10) REVERT: W 61 PHE cc_start: 0.9434 (t80) cc_final: 0.9133 (t80) REVERT: W 89 MET cc_start: 0.9228 (mtt) cc_final: 0.8940 (mtp) REVERT: W 108 GLN cc_start: 0.8501 (pp30) cc_final: 0.7765 (mt0) REVERT: W 132 PHE cc_start: 0.9224 (t80) cc_final: 0.8613 (t80) REVERT: W 136 ASN cc_start: 0.8915 (m-40) cc_final: 0.8409 (m110) REVERT: W 142 PHE cc_start: 0.8711 (t80) cc_final: 0.8477 (t80) REVERT: W 176 MET cc_start: 0.9204 (mmm) cc_final: 0.8848 (tpt) REVERT: W 196 TRP cc_start: 0.9594 (t60) cc_final: 0.9145 (t60) outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.1188 time to fit residues: 25.1631 Evaluate side-chains 138 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain W residue 86 HIS Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 160 MET Chi-restraints excluded: chain W residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 17 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN W 84 GLN ** W 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.051718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038877 restraints weight = 69298.766| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.04 r_work: 0.2707 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16268 Z= 0.247 Angle : 0.639 9.543 22077 Z= 0.310 Chirality : 0.047 0.221 2454 Planarity : 0.004 0.052 2816 Dihedral : 7.674 179.877 2255 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.59 % Allowed : 6.47 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.69 (0.20), residues: 1987 helix: 0.99 (0.18), residues: 904 sheet: 0.14 (0.28), residues: 352 loop : 0.15 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.027 0.001 TYR W 210 PHE 0.010 0.001 PHE C 127 TRP 0.010 0.001 TRP B 79 HIS 0.008 0.001 HIS W 193 Details of bonding type rmsd covalent geometry : bond 0.00580 (16268) covalent geometry : angle 0.63850 (22077) hydrogen bonds : bond 0.03152 ( 756) hydrogen bonds : angle 4.39089 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3974 Ramachandran restraints generated. 1987 Oldfield, 0 Emsley, 1987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9521 (mmm) cc_final: 0.9207 (mmt) REVERT: A 132 MET cc_start: 0.8962 (tmm) cc_final: 0.8660 (tmm) REVERT: B 118 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8602 (mmmt) REVERT: B 360 GLN cc_start: 0.8973 (mp10) cc_final: 0.8720 (pm20) REVERT: C 47 MET cc_start: 0.7236 (pmm) cc_final: 0.6545 (pmm) REVERT: E 47 MET cc_start: 0.7583 (pmm) cc_final: 0.7260 (pmm) REVERT: E 305 MET cc_start: 0.9445 (mmm) cc_final: 0.9226 (mmm) REVERT: E 355 MET cc_start: 0.9166 (mtp) cc_final: 0.8955 (mmm) REVERT: W 57 TYR cc_start: 0.8810 (p90) cc_final: 0.8499 (p90) REVERT: W 59 GLN cc_start: 0.9174 (mt0) cc_final: 0.8865 (mp10) REVERT: W 61 PHE cc_start: 0.9431 (t80) cc_final: 0.9153 (t80) REVERT: W 89 MET cc_start: 0.9232 (mtt) cc_final: 0.8934 (mtp) REVERT: W 108 GLN cc_start: 0.8492 (pp30) cc_final: 0.7739 (mt0) REVERT: W 132 PHE cc_start: 0.9235 (t80) cc_final: 0.8644 (t80) REVERT: W 136 ASN cc_start: 0.8967 (m-40) cc_final: 0.8444 (m110) REVERT: W 142 PHE cc_start: 0.8773 (t80) cc_final: 0.8549 (t80) REVERT: W 176 MET cc_start: 0.9230 (mmm) cc_final: 0.8880 (tpt) REVERT: W 196 TRP cc_start: 0.9594 (t60) cc_final: 0.9193 (t60) REVERT: W 210 TYR cc_start: 0.8767 (t80) cc_final: 0.8430 (t80) outliers start: 10 outliers final: 8 residues processed: 138 average time/residue: 0.1127 time to fit residues: 24.3656 Evaluate side-chains 137 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain W residue 86 HIS Chi-restraints excluded: chain W residue 115 LEU Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 160 MET Chi-restraints excluded: chain W residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 129 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 GLN ** W 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.039556 restraints weight = 68375.722| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.03 r_work: 0.2735 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16268 Z= 0.140 Angle : 0.597 10.697 22077 Z= 0.284 Chirality : 0.045 0.211 2454 Planarity : 0.003 0.052 2816 Dihedral : 7.538 179.405 2255 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.53 % Allowed : 6.76 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.79 (0.20), residues: 1987 helix: 1.07 (0.18), residues: 904 sheet: 0.20 (0.28), residues: 346 loop : 0.19 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.024 0.001 TYR W 210 PHE 0.015 0.001 PHE D 124 TRP 0.012 0.001 TRP B 86 HIS 0.007 0.001 HIS W 193 Details of bonding type rmsd covalent geometry : bond 0.00328 (16268) covalent geometry : angle 0.59678 (22077) hydrogen bonds : bond 0.02772 ( 756) hydrogen bonds : angle 4.27815 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.55 seconds wall clock time: 68 minutes 13.20 seconds (4093.20 seconds total)