Starting phenix.real_space_refine on Mon Apr 6 10:17:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.map" model { file = "/net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xye_72330/04_2026/9xye_72330.cif" } resolution = 3.18 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 115 5.16 5 C 10983 2.51 5 N 2926 2.21 5 O 3317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 17356 Number of models: 1 Model: "" Number of chains: 12 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: 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: "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: "X" 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: 3.53, per 1000 atoms: 0.20 Number of scatterers: 17356 At special positions: 0 Unit cell: (89.424, 98.532, 211.968, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 3317 8.00 N 2926 7.00 C 10983 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: 1.34 Conformation dependent library (CDL) restraints added in 636.2 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4082 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 54.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.508A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.732A 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: 3.860A 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 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.646A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.609A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.092A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.565A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.757A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 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 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.717A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.826A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.720A pdb=" N LEU B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.870A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.859A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.674A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.996A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.668A 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 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 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.593A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.972A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.512A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.566A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.933A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.749A 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 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.013A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.634A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.050A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (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 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.601A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.020A 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 194 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.693A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.752A 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 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.170A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.728A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.967A 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 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.541A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.588A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.520A 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: 4.136A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.731A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.724A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.711A 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 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.028A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.576A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.070A 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 369 through 374 Processing helix chain 'W' and resid 41 through 53 Processing helix chain 'W' and resid 53 through 66 removed outlier: 3.549A pdb=" N GLY W 66 " --> pdb=" O SER W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 92 removed outlier: 3.850A pdb=" N LYS W 71 " --> pdb=" O GLY W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 122 Proline residue: W 107 - end of helix Processing helix chain 'W' and resid 127 through 136 removed outlier: 3.564A pdb=" N LEU W 131 " --> pdb=" O LEU W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 146 removed outlier: 4.249A pdb=" N VAL W 144 " --> pdb=" O LEU W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 173 removed outlier: 3.985A pdb=" N TYR W 164 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG W 167 " --> pdb=" O PHE W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 200 removed outlier: 4.076A pdb=" N VAL W 180 " --> pdb=" O ASP W 176 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP W 190 " --> pdb=" O TYR W 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 53 Processing helix chain 'X' and resid 53 through 66 Processing helix chain 'X' and resid 67 through 93 removed outlier: 3.525A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET X 75 " --> pdb=" O LYS X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 122 Proline residue: X 107 - end of helix removed outlier: 3.789A pdb=" N ASN X 122 " --> pdb=" O PHE X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 136 removed outlier: 3.605A pdb=" N LEU X 131 " --> pdb=" O LEU X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 146 removed outlier: 3.603A pdb=" N ALA X 140 " --> pdb=" O SER X 137 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL X 144 " --> pdb=" O LEU X 141 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET X 146 " --> pdb=" O TRP X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 172 removed outlier: 4.063A pdb=" N TYR X 164 " --> pdb=" O ALA X 160 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG X 167 " --> pdb=" O PHE X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 201 removed outlier: 4.141A pdb=" N VAL X 180 " --> pdb=" O ASP X 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.804A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 7.022A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.488A 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: 3.819A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.485A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 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: 7.131A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.465A 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: 3.873A 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 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.593A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.589A 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: 6.031A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.115A 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: 3.710A 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: 6.575A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.257A 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 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: 3.944A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (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: 6.064A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.160A 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 241 895 hydrogen bonds defined for protein. 2376 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: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4512 1.33 - 1.46: 4125 1.46 - 1.58: 8883 1.58 - 1.71: 15 1.71 - 1.83: 203 Bond restraints: 17738 Sorted by residual: bond pdb=" C ALA W 147 " pdb=" N PRO W 148 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.34e-02 1.83e+03 1.90e+01 bond pdb=" C ALA X 147 " pdb=" N PRO X 148 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.34e-02 1.83e+03 1.89e+01 bond pdb=" CG1 ILE W 61 " pdb=" CD1 ILE W 61 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.21e+01 bond pdb=" C VAL W 69 " pdb=" N GLN W 70 " ideal model delta sigma weight residual 1.334 1.370 -0.036 1.20e-02 6.94e+03 9.09e+00 bond pdb=" CA THR A 203 " pdb=" C THR A 203 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.66e-02 3.63e+03 7.88e+00 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 23039 2.91 - 5.82: 845 5.82 - 8.73: 136 8.73 - 11.64: 40 11.64 - 14.55: 5 Bond angle restraints: 24065 Sorted by residual: angle pdb=" C MET W 146 " pdb=" N ALA W 147 " pdb=" CA ALA W 147 " ideal model delta sigma weight residual 122.29 136.84 -14.55 1.48e+00 4.57e-01 9.66e+01 angle pdb=" CA ALA W 147 " pdb=" C ALA W 147 " pdb=" N PRO W 148 " ideal model delta sigma weight residual 117.69 124.73 -7.04 9.30e-01 1.16e+00 5.73e+01 angle pdb=" C MET X 146 " pdb=" N ALA X 147 " pdb=" CA ALA X 147 " ideal model delta sigma weight residual 122.29 132.86 -10.57 1.48e+00 4.57e-01 5.10e+01 angle pdb=" N GLN W 194 " pdb=" CA GLN W 194 " pdb=" CB GLN W 194 " ideal model delta sigma weight residual 110.30 119.69 -9.39 1.54e+00 4.22e-01 3.72e+01 angle pdb=" CA ALA X 147 " pdb=" C ALA X 147 " pdb=" N PRO X 148 " ideal model delta sigma weight residual 117.69 123.21 -5.52 9.30e-01 1.16e+00 3.52e+01 ... (remaining 24060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 10531 35.26 - 70.53: 112 70.53 - 105.79: 17 105.79 - 141.06: 7 141.06 - 176.32: 2 Dihedral angle restraints: 10669 sinusoidal: 4301 harmonic: 6368 Sorted by residual: dihedral pdb=" CA GLN A 49 " pdb=" C GLN A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta harmonic sigma weight residual 180.00 132.59 47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA ALA X 147 " pdb=" C ALA X 147 " pdb=" N PRO X 148 " pdb=" CA PRO X 148 " ideal model delta harmonic sigma weight residual -180.00 -136.65 -43.35 0 5.00e+00 4.00e-02 7.52e+01 dihedral pdb=" C5' ADP B 400 " pdb=" O5' ADP B 400 " pdb=" PA ADP B 400 " pdb=" O2A ADP B 400 " ideal model delta sinusoidal sigma weight residual -60.00 116.32 -176.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 10666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2481 0.123 - 0.247: 170 0.247 - 0.370: 17 0.370 - 0.493: 4 0.493 - 0.616: 1 Chirality restraints: 2673 Sorted by residual: chirality pdb=" CB ILE X 138 " pdb=" CA ILE X 138 " pdb=" CG1 ILE X 138 " pdb=" CG2 ILE X 138 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.62 2.00e-01 2.50e+01 9.49e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 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 -2.24 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 2670 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE X 47 " 0.028 2.00e-02 2.50e+03 4.02e-02 2.83e+01 pdb=" CG PHE X 47 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE X 47 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE X 47 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE X 47 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE X 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE X 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 182 " 0.032 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP W 182 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP W 182 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP W 182 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP W 182 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP W 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP W 182 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 182 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 182 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP W 182 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 37 " 0.060 5.00e-02 4.00e+02 9.30e-02 1.39e+01 pdb=" N PRO A 38 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.050 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 34 2.64 - 3.21: 14470 3.21 - 3.77: 27213 3.77 - 4.34: 37884 4.34 - 4.90: 62126 Nonbonded interactions: 141727 Sorted by model distance: nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.079 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.082 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.143 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.177 2.170 nonbonded pdb=" O2B ADP B 400 " pdb="MG MG B 401 " model vdw 2.224 2.170 ... (remaining 141722 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'W' selection = chain 'X' } 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: 5.130 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.950 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 17738 Z= 0.336 Angle : 1.309 14.549 24065 Z= 0.702 Chirality : 0.072 0.616 2673 Planarity : 0.010 0.099 3067 Dihedral : 13.232 176.319 6587 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.14 % 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: -2.71 (0.15), residues: 2170 helix: -2.30 (0.12), residues: 1069 sheet: -0.41 (0.30), residues: 275 loop : -1.29 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 95 TYR 0.036 0.003 TYR X 172 PHE 0.092 0.004 PHE X 47 TRP 0.068 0.004 TRP W 182 HIS 0.029 0.003 HIS W 72 Details of bonding type rmsd covalent geometry : bond 0.00728 (17738) covalent geometry : angle 1.30934 (24065) hydrogen bonds : bond 0.15927 ( 887) hydrogen bonds : angle 7.25167 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.5134 (mtp) cc_final: 0.4637 (mtp) REVERT: A 123 MET cc_start: 0.9355 (mmp) cc_final: 0.8996 (mmp) REVERT: A 227 MET cc_start: 0.9539 (mmm) cc_final: 0.9318 (mmm) REVERT: A 269 MET cc_start: 0.8776 (mtm) cc_final: 0.8416 (mtm) REVERT: A 283 MET cc_start: 0.8861 (mmt) cc_final: 0.8657 (mmp) REVERT: A 355 MET cc_start: 0.8847 (pmm) cc_final: 0.8609 (pmm) REVERT: B 40 HIS cc_start: 0.8455 (m90) cc_final: 0.8185 (m90) REVERT: B 132 MET cc_start: 0.7459 (ttp) cc_final: 0.7202 (ttp) REVERT: B 325 MET cc_start: 0.8371 (mmt) cc_final: 0.7902 (mpp) REVERT: B 360 GLN cc_start: 0.9228 (mp10) cc_final: 0.8885 (mp10) REVERT: C 132 MET cc_start: 0.8684 (ptm) cc_final: 0.8379 (ppp) REVERT: C 325 MET cc_start: 0.8318 (mtp) cc_final: 0.8112 (mtp) REVERT: D 123 MET cc_start: 0.9413 (mmt) cc_final: 0.8990 (mmt) REVERT: D 176 MET cc_start: 0.9065 (mtt) cc_final: 0.8721 (mtt) REVERT: E 47 MET cc_start: 0.7760 (ptm) cc_final: 0.7215 (pmm) REVERT: E 299 MET cc_start: 0.8963 (mtp) cc_final: 0.8520 (ttp) REVERT: E 313 MET cc_start: 0.9048 (tpp) cc_final: 0.8721 (ttm) REVERT: W 43 TYR cc_start: 0.8846 (p90) cc_final: 0.8543 (p90) REVERT: W 47 PHE cc_start: 0.9686 (t80) cc_final: 0.9254 (t80) REVERT: W 77 HIS cc_start: 0.9619 (t70) cc_final: 0.9275 (t70) REVERT: W 139 GLN cc_start: 0.8801 (mp10) cc_final: 0.7990 (mp10) REVERT: W 153 TYR cc_start: 0.9229 (t80) cc_final: 0.7835 (t80) REVERT: W 157 MET cc_start: 0.9288 (mmp) cc_final: 0.8423 (tpp) REVERT: W 158 ASN cc_start: 0.9530 (t0) cc_final: 0.9090 (t0) REVERT: W 162 MET cc_start: 0.9282 (mtp) cc_final: 0.8886 (mmm) REVERT: W 167 ARG cc_start: 0.9098 (mtt90) cc_final: 0.8607 (mtt-85) REVERT: W 179 HIS cc_start: 0.9364 (m90) cc_final: 0.9066 (m90) REVERT: W 190 TRP cc_start: 0.8911 (m-90) cc_final: 0.8701 (m-90) REVERT: X 43 TYR cc_start: 0.9050 (p90) cc_final: 0.8772 (p90) REVERT: X 58 TYR cc_start: 0.9234 (t80) cc_final: 0.9002 (t80) REVERT: X 75 MET cc_start: 0.8176 (tpt) cc_final: 0.7963 (tpt) REVERT: X 76 VAL cc_start: 0.9350 (t) cc_final: 0.9082 (t) REVERT: X 77 HIS cc_start: 0.8850 (t70) cc_final: 0.8520 (t-170) REVERT: X 111 GLN cc_start: 0.9337 (tp40) cc_final: 0.9119 (tp40) REVERT: X 118 PHE cc_start: 0.9368 (t80) cc_final: 0.8958 (t80) REVERT: X 129 ASN cc_start: 0.8978 (t0) cc_final: 0.8731 (t0) REVERT: X 153 TYR cc_start: 0.9510 (t80) cc_final: 0.9151 (t80) REVERT: X 157 MET cc_start: 0.7871 (mmp) cc_final: 0.6824 (mmt) REVERT: X 158 ASN cc_start: 0.9509 (t0) cc_final: 0.9277 (t0) REVERT: X 182 TRP cc_start: 0.9462 (t60) cc_final: 0.8871 (t-100) REVERT: X 190 TRP cc_start: 0.9198 (m100) cc_final: 0.8077 (m100) REVERT: X 194 GLN cc_start: 0.9304 (mt0) cc_final: 0.8462 (mm-40) REVERT: X 200 PHE cc_start: 0.9232 (m-80) cc_final: 0.8930 (m-80) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1307 time to fit residues: 39.4958 Evaluate side-chains 172 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 173 HIS A 263 GLN A 371 HIS B 49 GLN B 371 HIS E 246 GLN W 94 GLN ** X 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 139 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041185 restraints weight = 129873.918| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.77 r_work: 0.2907 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17738 Z= 0.172 Angle : 0.665 9.401 24065 Z= 0.335 Chirality : 0.045 0.150 2673 Planarity : 0.005 0.063 3067 Dihedral : 10.144 179.388 2449 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.49 % Allowed : 3.67 % Favored : 95.84 % 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: -0.84 (0.18), residues: 2170 helix: -0.42 (0.15), residues: 1052 sheet: -0.19 (0.30), residues: 290 loop : -0.63 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 372 TYR 0.017 0.001 TYR W 153 PHE 0.017 0.001 PHE W 118 TRP 0.025 0.002 TRP X 182 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00375 (17738) covalent geometry : angle 0.66482 (24065) hydrogen bonds : bond 0.03647 ( 887) hydrogen bonds : angle 5.01915 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8986 (mp10) cc_final: 0.8744 (mp10) REVERT: A 82 MET cc_start: 0.8932 (tpp) cc_final: 0.8715 (tpp) REVERT: A 269 MET cc_start: 0.8894 (mtm) cc_final: 0.8180 (mtm) REVERT: A 305 MET cc_start: 0.8652 (mmm) cc_final: 0.8441 (mmm) REVERT: B 40 HIS cc_start: 0.8485 (m90) cc_final: 0.8136 (m-70) REVERT: B 44 MET cc_start: 0.4279 (tmm) cc_final: 0.4058 (tmm) REVERT: B 49 GLN cc_start: 0.6634 (mt0) cc_final: 0.6279 (mt0) REVERT: C 44 MET cc_start: 0.9176 (tpp) cc_final: 0.8855 (mmm) REVERT: C 47 MET cc_start: 0.8048 (ppp) cc_final: 0.7501 (pmm) REVERT: C 227 MET cc_start: 0.8787 (mmm) cc_final: 0.8581 (mmm) REVERT: C 325 MET cc_start: 0.8450 (mtp) cc_final: 0.8051 (mtp) REVERT: D 123 MET cc_start: 0.9447 (mmt) cc_final: 0.9015 (mmt) REVERT: E 47 MET cc_start: 0.8065 (ptm) cc_final: 0.7670 (ptp) REVERT: W 43 TYR cc_start: 0.8938 (p90) cc_final: 0.8470 (p90) REVERT: W 47 PHE cc_start: 0.9676 (t80) cc_final: 0.9210 (t80) REVERT: W 77 HIS cc_start: 0.9615 (t70) cc_final: 0.9375 (t70) REVERT: W 84 ARG cc_start: 0.9148 (ptm-80) cc_final: 0.8771 (ptm160) REVERT: W 122 ASN cc_start: 0.8688 (p0) cc_final: 0.7914 (p0) REVERT: W 139 GLN cc_start: 0.8697 (mp10) cc_final: 0.8394 (mp10) REVERT: W 143 TRP cc_start: 0.9451 (p-90) cc_final: 0.9034 (p-90) REVERT: W 153 TYR cc_start: 0.8861 (t80) cc_final: 0.8183 (t80) REVERT: W 157 MET cc_start: 0.9024 (mmp) cc_final: 0.8642 (mmp) REVERT: W 158 ASN cc_start: 0.9489 (t0) cc_final: 0.9285 (m-40) REVERT: W 167 ARG cc_start: 0.9125 (mtt90) cc_final: 0.8691 (mtt-85) REVERT: W 179 HIS cc_start: 0.9349 (m90) cc_final: 0.9075 (m90) REVERT: W 182 TRP cc_start: 0.8950 (t-100) cc_final: 0.8592 (t-100) REVERT: W 196 TYR cc_start: 0.9437 (t80) cc_final: 0.9233 (t80) REVERT: X 43 TYR cc_start: 0.9145 (p90) cc_final: 0.8865 (p90) REVERT: X 68 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8654 (p0) REVERT: X 75 MET cc_start: 0.8297 (tpt) cc_final: 0.8040 (tpt) REVERT: X 76 VAL cc_start: 0.9403 (t) cc_final: 0.9192 (t) REVERT: X 77 HIS cc_start: 0.8830 (t70) cc_final: 0.8616 (t-170) REVERT: X 157 MET cc_start: 0.7423 (mmp) cc_final: 0.7214 (mmm) REVERT: X 194 GLN cc_start: 0.8925 (mt0) cc_final: 0.8492 (mm110) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.1224 time to fit residues: 34.5315 Evaluate side-chains 168 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain W residue 58 TYR Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 130 HIS Chi-restraints excluded: chain X residue 68 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 173 HIS W 72 HIS ** X 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.051316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040921 restraints weight = 133037.304| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.79 r_work: 0.2884 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17738 Z= 0.162 Angle : 0.617 8.128 24065 Z= 0.306 Chirality : 0.045 0.144 2673 Planarity : 0.004 0.050 3067 Dihedral : 9.359 179.860 2449 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.03 % Allowed : 4.91 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2170 helix: 0.34 (0.16), residues: 1054 sheet: 0.06 (0.30), residues: 300 loop : -0.46 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 119 TYR 0.026 0.001 TYR X 196 PHE 0.020 0.001 PHE W 118 TRP 0.012 0.001 TRP X 182 HIS 0.004 0.001 HIS X 201 Details of bonding type rmsd covalent geometry : bond 0.00363 (17738) covalent geometry : angle 0.61691 (24065) hydrogen bonds : bond 0.03151 ( 887) hydrogen bonds : angle 4.67907 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8997 (tpp) cc_final: 0.8733 (tpp) REVERT: A 132 MET cc_start: 0.8696 (tpp) cc_final: 0.8469 (tpp) REVERT: A 227 MET cc_start: 0.9386 (mmm) cc_final: 0.9160 (mmm) REVERT: A 269 MET cc_start: 0.8960 (mtm) cc_final: 0.8230 (mtm) REVERT: A 355 MET cc_start: 0.8883 (pmm) cc_final: 0.8589 (pmm) REVERT: B 40 HIS cc_start: 0.8498 (m90) cc_final: 0.8135 (m90) REVERT: B 44 MET cc_start: 0.4513 (tmm) cc_final: 0.4227 (tmm) REVERT: B 82 MET cc_start: 0.9141 (tpt) cc_final: 0.8811 (mmm) REVERT: B 132 MET cc_start: 0.7382 (tmm) cc_final: 0.7155 (tmm) REVERT: C 44 MET cc_start: 0.9270 (tpp) cc_final: 0.9065 (mmm) REVERT: C 123 MET cc_start: 0.8934 (mmm) cc_final: 0.8587 (mmm) REVERT: C 132 MET cc_start: 0.8883 (ptm) cc_final: 0.8596 (ppp) REVERT: D 123 MET cc_start: 0.9431 (mmt) cc_final: 0.8967 (mmt) REVERT: E 47 MET cc_start: 0.8248 (ptm) cc_final: 0.7907 (ptp) REVERT: W 43 TYR cc_start: 0.8907 (p90) cc_final: 0.8477 (p90) REVERT: W 47 PHE cc_start: 0.9670 (t80) cc_final: 0.9204 (t80) REVERT: W 77 HIS cc_start: 0.9600 (t70) cc_final: 0.9350 (t70) REVERT: W 84 ARG cc_start: 0.9169 (ptm-80) cc_final: 0.8724 (ptm160) REVERT: W 127 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8586 (pt) REVERT: W 139 GLN cc_start: 0.8690 (mp10) cc_final: 0.8303 (mp10) REVERT: W 143 TRP cc_start: 0.9397 (p-90) cc_final: 0.8772 (p-90) REVERT: W 153 TYR cc_start: 0.8771 (t80) cc_final: 0.8187 (t80) REVERT: W 179 HIS cc_start: 0.9336 (m90) cc_final: 0.9057 (m90) REVERT: W 182 TRP cc_start: 0.9010 (t-100) cc_final: 0.8618 (t-100) REVERT: W 196 TYR cc_start: 0.9487 (t80) cc_final: 0.9226 (t80) REVERT: W 197 ILE cc_start: 0.9635 (mm) cc_final: 0.9172 (tp) REVERT: X 43 TYR cc_start: 0.9242 (p90) cc_final: 0.8878 (p90) REVERT: X 118 PHE cc_start: 0.9403 (t80) cc_final: 0.9140 (t80) REVERT: X 194 GLN cc_start: 0.8831 (mt0) cc_final: 0.8592 (mm110) outliers start: 19 outliers final: 6 residues processed: 177 average time/residue: 0.1156 time to fit residues: 32.7905 Evaluate side-chains 170 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain W residue 58 TYR Chi-restraints excluded: chain W residue 119 ARG Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 130 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 81 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN C 41 GLN ** W 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.050982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040589 restraints weight = 131906.114| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.75 r_work: 0.2881 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17738 Z= 0.143 Angle : 0.597 10.218 24065 Z= 0.292 Chirality : 0.044 0.141 2673 Planarity : 0.004 0.068 3067 Dihedral : 8.668 179.252 2449 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.70 % Allowed : 6.15 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.19), residues: 2170 helix: 0.71 (0.17), residues: 1056 sheet: 0.21 (0.30), residues: 297 loop : -0.35 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 119 TYR 0.029 0.001 TYR X 196 PHE 0.021 0.001 PHE X 200 TRP 0.015 0.001 TRP W 207 HIS 0.011 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00318 (17738) covalent geometry : angle 0.59654 (24065) hydrogen bonds : bond 0.02881 ( 887) hydrogen bonds : angle 4.54573 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9018 (tpp) cc_final: 0.8716 (tpp) REVERT: A 132 MET cc_start: 0.8659 (tpp) cc_final: 0.7763 (tpp) REVERT: A 227 MET cc_start: 0.9376 (mmm) cc_final: 0.9115 (mmm) REVERT: A 269 MET cc_start: 0.9020 (mtm) cc_final: 0.8287 (mtm) REVERT: A 355 MET cc_start: 0.8857 (pmm) cc_final: 0.8598 (pmm) REVERT: B 40 HIS cc_start: 0.8463 (m90) cc_final: 0.8091 (m90) REVERT: B 44 MET cc_start: 0.4586 (tmm) cc_final: 0.4237 (tmm) REVERT: B 82 MET cc_start: 0.9185 (tpt) cc_final: 0.8830 (mmm) REVERT: B 132 MET cc_start: 0.7624 (tmm) cc_final: 0.7364 (tmm) REVERT: C 44 MET cc_start: 0.9312 (tpp) cc_final: 0.9098 (mmm) REVERT: C 123 MET cc_start: 0.8923 (mmm) cc_final: 0.8606 (mmm) REVERT: C 132 MET cc_start: 0.8882 (ptm) cc_final: 0.8672 (ppp) REVERT: D 44 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: D 123 MET cc_start: 0.9401 (mmt) cc_final: 0.8949 (mmt) REVERT: D 283 MET cc_start: 0.9097 (mmt) cc_final: 0.8821 (mpp) REVERT: E 47 MET cc_start: 0.8288 (ptm) cc_final: 0.8039 (ptp) REVERT: W 43 TYR cc_start: 0.8925 (p90) cc_final: 0.8502 (p90) REVERT: W 47 PHE cc_start: 0.9650 (t80) cc_final: 0.9161 (t80) REVERT: W 77 HIS cc_start: 0.9581 (t70) cc_final: 0.9270 (t70) REVERT: W 84 ARG cc_start: 0.9166 (ptm-80) cc_final: 0.8581 (ptm160) REVERT: W 127 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8683 (pt) REVERT: W 139 GLN cc_start: 0.8498 (mp10) cc_final: 0.8084 (mp10) REVERT: W 153 TYR cc_start: 0.8727 (t80) cc_final: 0.8136 (t80) REVERT: W 157 MET cc_start: 0.9123 (mmp) cc_final: 0.8594 (mmp) REVERT: W 179 HIS cc_start: 0.9349 (m90) cc_final: 0.9044 (m90) REVERT: W 182 TRP cc_start: 0.8989 (t-100) cc_final: 0.8644 (t-100) REVERT: W 196 TYR cc_start: 0.9475 (t80) cc_final: 0.9184 (t80) REVERT: W 197 ILE cc_start: 0.9643 (mm) cc_final: 0.9286 (tp) REVERT: X 43 TYR cc_start: 0.9283 (p90) cc_final: 0.8753 (p90) REVERT: X 118 PHE cc_start: 0.9400 (t80) cc_final: 0.9089 (t80) REVERT: X 157 MET cc_start: 0.7321 (mmm) cc_final: 0.7047 (mmm) REVERT: X 194 GLN cc_start: 0.8871 (mt0) cc_final: 0.8635 (mm110) outliers start: 13 outliers final: 7 residues processed: 170 average time/residue: 0.1221 time to fit residues: 32.7592 Evaluate side-chains 171 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 130 HIS Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain X residue 58 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 151 optimal weight: 0.0050 chunk 64 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN D 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.050614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040209 restraints weight = 130815.476| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.69 r_work: 0.2853 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.004 0.032 17738 Z= 0.169 Angle : 0.601 10.068 24065 Z= 0.294 Chirality : 0.044 0.144 2673 Planarity : 0.004 0.061 3067 Dihedral : 8.212 177.255 2449 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.86 % Allowed : 6.96 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 2170 helix: 0.89 (0.17), residues: 1062 sheet: 0.43 (0.30), residues: 315 loop : -0.32 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 119 TYR 0.022 0.001 TYR X 196 PHE 0.032 0.001 PHE X 200 TRP 0.034 0.002 TRP W 190 HIS 0.010 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00376 (17738) covalent geometry : angle 0.60090 (24065) hydrogen bonds : bond 0.02875 ( 887) hydrogen bonds : angle 4.47179 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9046 (tpp) cc_final: 0.8697 (tpp) REVERT: A 132 MET cc_start: 0.8682 (tpp) cc_final: 0.7792 (tpp) REVERT: A 227 MET cc_start: 0.9393 (mmm) cc_final: 0.9133 (mmm) REVERT: A 269 MET cc_start: 0.9078 (mtm) cc_final: 0.8387 (mtm) REVERT: B 40 HIS cc_start: 0.8418 (m90) cc_final: 0.8056 (m90) REVERT: B 44 MET cc_start: 0.4478 (tmm) cc_final: 0.4012 (tmm) REVERT: B 132 MET cc_start: 0.7837 (tmm) cc_final: 0.7539 (tmm) REVERT: C 44 MET cc_start: 0.9305 (tpp) cc_final: 0.9090 (mmm) REVERT: C 123 MET cc_start: 0.8935 (mmm) cc_final: 0.8713 (mmm) REVERT: C 176 MET cc_start: 0.8939 (mtt) cc_final: 0.8690 (mtt) REVERT: D 44 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: D 123 MET cc_start: 0.9384 (mmt) cc_final: 0.8991 (mmt) REVERT: D 283 MET cc_start: 0.9131 (mmt) cc_final: 0.8884 (mpp) REVERT: W 43 TYR cc_start: 0.8953 (p90) cc_final: 0.8555 (p90) REVERT: W 47 PHE cc_start: 0.9624 (t80) cc_final: 0.9105 (t80) REVERT: W 77 HIS cc_start: 0.9572 (t70) cc_final: 0.9349 (t-90) REVERT: W 84 ARG cc_start: 0.9149 (ptm-80) cc_final: 0.8606 (ptm160) REVERT: W 127 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8678 (pt) REVERT: W 129 ASN cc_start: 0.8510 (t0) cc_final: 0.8293 (t0) REVERT: W 139 GLN cc_start: 0.8601 (mp10) cc_final: 0.8180 (mp10) REVERT: W 153 TYR cc_start: 0.8713 (t80) cc_final: 0.8089 (t80) REVERT: W 157 MET cc_start: 0.9214 (mmp) cc_final: 0.8625 (mmp) REVERT: W 179 HIS cc_start: 0.9370 (m90) cc_final: 0.9093 (m-70) REVERT: W 182 TRP cc_start: 0.9015 (t-100) cc_final: 0.8762 (t-100) REVERT: W 190 TRP cc_start: 0.9276 (m100) cc_final: 0.9037 (m100) REVERT: W 196 TYR cc_start: 0.9437 (t80) cc_final: 0.9093 (t80) REVERT: W 197 ILE cc_start: 0.9627 (mm) cc_final: 0.9255 (tp) REVERT: X 75 MET cc_start: 0.8126 (tpt) cc_final: 0.7863 (tpt) REVERT: X 118 PHE cc_start: 0.9405 (t80) cc_final: 0.9066 (t80) REVERT: X 119 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6472 (ttt180) REVERT: X 146 MET cc_start: 0.7222 (ptt) cc_final: 0.6712 (pmm) REVERT: X 157 MET cc_start: 0.7692 (mmm) cc_final: 0.7450 (mmm) REVERT: X 194 GLN cc_start: 0.8892 (mt0) cc_final: 0.8648 (mm110) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 0.1208 time to fit residues: 33.1619 Evaluate side-chains 170 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 130 HIS Chi-restraints excluded: chain W residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 246 GLN ** W 111 GLN ** 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 = 0.3476 r_free = 0.3476 target = 0.050655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040272 restraints weight = 130570.120| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.70 r_work: 0.2863 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.151 Angle : 0.596 10.457 24065 Z= 0.290 Chirality : 0.044 0.145 2673 Planarity : 0.004 0.061 3067 Dihedral : 7.956 173.902 2449 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.86 % Allowed : 7.34 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2170 helix: 0.94 (0.17), residues: 1074 sheet: 0.42 (0.29), residues: 315 loop : -0.27 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 119 TYR 0.024 0.001 TYR X 196 PHE 0.015 0.001 PHE W 118 TRP 0.011 0.001 TRP X 182 HIS 0.009 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00338 (17738) covalent geometry : angle 0.59621 (24065) hydrogen bonds : bond 0.02764 ( 887) hydrogen bonds : angle 4.42157 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9066 (tpp) cc_final: 0.8728 (tpp) REVERT: A 132 MET cc_start: 0.8567 (tpp) cc_final: 0.7771 (tpp) REVERT: A 227 MET cc_start: 0.9404 (mmm) cc_final: 0.9144 (mmm) REVERT: A 269 MET cc_start: 0.9066 (mtm) cc_final: 0.8421 (mtm) REVERT: B 40 HIS cc_start: 0.8396 (m90) cc_final: 0.7983 (m-70) REVERT: B 44 MET cc_start: 0.4547 (tmm) cc_final: 0.4115 (tmm) REVERT: B 132 MET cc_start: 0.7913 (tmm) cc_final: 0.7552 (tmm) REVERT: C 44 MET cc_start: 0.9387 (tpp) cc_final: 0.9139 (mmm) REVERT: C 176 MET cc_start: 0.8927 (mtt) cc_final: 0.8658 (mtt) REVERT: C 325 MET cc_start: 0.8514 (mmm) cc_final: 0.8249 (mmm) REVERT: D 44 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7685 (mpp) REVERT: D 123 MET cc_start: 0.9383 (mmt) cc_final: 0.8956 (mmt) REVERT: E 355 MET cc_start: 0.9094 (mtm) cc_final: 0.8779 (mmp) REVERT: W 43 TYR cc_start: 0.8969 (p90) cc_final: 0.8560 (p90) REVERT: W 47 PHE cc_start: 0.9625 (t80) cc_final: 0.9139 (t80) REVERT: W 77 HIS cc_start: 0.9579 (t70) cc_final: 0.9307 (t-90) REVERT: W 84 ARG cc_start: 0.9091 (ptm-80) cc_final: 0.8661 (ptm160) REVERT: W 127 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8709 (pt) REVERT: W 129 ASN cc_start: 0.8481 (t0) cc_final: 0.8264 (t0) REVERT: W 139 GLN cc_start: 0.8644 (mp10) cc_final: 0.8159 (mp10) REVERT: W 153 TYR cc_start: 0.8779 (t80) cc_final: 0.8066 (t80) REVERT: W 157 MET cc_start: 0.9209 (mmp) cc_final: 0.8609 (mmp) REVERT: W 179 HIS cc_start: 0.9353 (m90) cc_final: 0.9066 (m-70) REVERT: W 182 TRP cc_start: 0.8972 (t-100) cc_final: 0.8622 (t-100) REVERT: W 190 TRP cc_start: 0.9268 (m100) cc_final: 0.9050 (m100) REVERT: W 196 TYR cc_start: 0.9467 (t80) cc_final: 0.9117 (t80) REVERT: W 197 ILE cc_start: 0.9648 (mm) cc_final: 0.9320 (tp) REVERT: X 75 MET cc_start: 0.8141 (tpt) cc_final: 0.7807 (tpt) REVERT: X 118 PHE cc_start: 0.9387 (t80) cc_final: 0.9056 (t80) REVERT: X 146 MET cc_start: 0.7299 (ptt) cc_final: 0.6773 (pmm) REVERT: X 157 MET cc_start: 0.7673 (mmm) cc_final: 0.7472 (mmm) REVERT: X 194 GLN cc_start: 0.8866 (mt0) cc_final: 0.8638 (mm110) outliers start: 16 outliers final: 7 residues processed: 170 average time/residue: 0.1218 time to fit residues: 32.7503 Evaluate side-chains 168 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN E 173 HIS ** W 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.051062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040618 restraints weight = 129547.427| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.67 r_work: 0.2880 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17738 Z= 0.106 Angle : 0.578 9.476 24065 Z= 0.280 Chirality : 0.043 0.148 2673 Planarity : 0.004 0.060 3067 Dihedral : 7.735 169.707 2449 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.76 % Allowed : 7.66 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2170 helix: 1.06 (0.17), residues: 1065 sheet: 0.50 (0.30), residues: 299 loop : -0.04 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 119 TYR 0.021 0.001 TYR X 196 PHE 0.029 0.001 PHE W 118 TRP 0.011 0.001 TRP X 182 HIS 0.009 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00236 (17738) covalent geometry : angle 0.57831 (24065) hydrogen bonds : bond 0.02663 ( 887) hydrogen bonds : angle 4.34418 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9056 (tpp) cc_final: 0.8684 (tpp) REVERT: A 132 MET cc_start: 0.8611 (tpp) cc_final: 0.7747 (tpp) REVERT: A 227 MET cc_start: 0.9404 (mmm) cc_final: 0.9149 (mmm) REVERT: A 269 MET cc_start: 0.9090 (mtm) cc_final: 0.8445 (mtm) REVERT: A 355 MET cc_start: 0.8855 (pmm) cc_final: 0.8597 (pmm) REVERT: B 40 HIS cc_start: 0.8385 (m90) cc_final: 0.8029 (m90) REVERT: B 44 MET cc_start: 0.4435 (tmm) cc_final: 0.3979 (tmm) REVERT: B 132 MET cc_start: 0.7936 (tmm) cc_final: 0.7603 (tmm) REVERT: C 44 MET cc_start: 0.9327 (tpp) cc_final: 0.9113 (mmm) REVERT: C 176 MET cc_start: 0.8918 (mtt) cc_final: 0.8634 (mtt) REVERT: C 325 MET cc_start: 0.8453 (mmm) cc_final: 0.8037 (mmm) REVERT: D 44 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: D 123 MET cc_start: 0.9380 (mmt) cc_final: 0.8964 (mmt) REVERT: E 355 MET cc_start: 0.9089 (mtm) cc_final: 0.8842 (mmp) REVERT: W 43 TYR cc_start: 0.8957 (p90) cc_final: 0.8541 (p90) REVERT: W 47 PHE cc_start: 0.9601 (t80) cc_final: 0.9079 (t80) REVERT: W 77 HIS cc_start: 0.9566 (t70) cc_final: 0.9332 (t-90) REVERT: W 84 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8664 (ptm160) REVERT: W 127 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8677 (pt) REVERT: W 129 ASN cc_start: 0.8525 (t0) cc_final: 0.8284 (t0) REVERT: W 139 GLN cc_start: 0.8825 (mp10) cc_final: 0.8301 (mp10) REVERT: W 153 TYR cc_start: 0.8672 (t80) cc_final: 0.7960 (t80) REVERT: W 157 MET cc_start: 0.9215 (mmp) cc_final: 0.8188 (mmt) REVERT: W 179 HIS cc_start: 0.9363 (m90) cc_final: 0.9080 (m-70) REVERT: W 182 TRP cc_start: 0.8994 (t-100) cc_final: 0.8608 (t-100) REVERT: W 190 TRP cc_start: 0.9229 (m100) cc_final: 0.8995 (m100) REVERT: W 196 TYR cc_start: 0.9468 (t80) cc_final: 0.9119 (t80) REVERT: W 197 ILE cc_start: 0.9644 (mm) cc_final: 0.9298 (tp) REVERT: X 118 PHE cc_start: 0.9410 (t80) cc_final: 0.9070 (t80) REVERT: X 146 MET cc_start: 0.7079 (ptt) cc_final: 0.6721 (pmm) REVERT: X 153 TYR cc_start: 0.9522 (t80) cc_final: 0.9287 (t80) REVERT: X 157 MET cc_start: 0.7687 (mmm) cc_final: 0.5599 (mmm) REVERT: X 194 GLN cc_start: 0.8895 (mt0) cc_final: 0.8654 (mm110) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 0.1123 time to fit residues: 30.3891 Evaluate side-chains 171 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 130 HIS Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 72 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 62 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** 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 = 0.3485 r_free = 0.3485 target = 0.050955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040576 restraints weight = 130672.869| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.69 r_work: 0.2884 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17738 Z= 0.118 Angle : 0.592 15.423 24065 Z= 0.286 Chirality : 0.043 0.177 2673 Planarity : 0.003 0.047 3067 Dihedral : 7.547 164.723 2449 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.92 % Allowed : 7.93 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.19), residues: 2170 helix: 1.10 (0.17), residues: 1065 sheet: 0.51 (0.30), residues: 309 loop : -0.01 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.020 0.001 TYR X 196 PHE 0.026 0.001 PHE W 118 TRP 0.012 0.001 TRP X 182 HIS 0.010 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00267 (17738) covalent geometry : angle 0.59222 (24065) hydrogen bonds : bond 0.02658 ( 887) hydrogen bonds : angle 4.33403 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9079 (tpp) cc_final: 0.8832 (tpp) REVERT: A 132 MET cc_start: 0.8525 (tpp) cc_final: 0.7742 (tpp) REVERT: A 227 MET cc_start: 0.9411 (mmm) cc_final: 0.9168 (mmm) REVERT: A 269 MET cc_start: 0.9102 (mtm) cc_final: 0.8462 (mtm) REVERT: A 355 MET cc_start: 0.8873 (pmm) cc_final: 0.8624 (pmm) REVERT: B 40 HIS cc_start: 0.8332 (m90) cc_final: 0.7992 (m90) REVERT: B 44 MET cc_start: 0.4532 (tmm) cc_final: 0.4036 (tmm) REVERT: B 132 MET cc_start: 0.7973 (tmm) cc_final: 0.7620 (tmm) REVERT: C 44 MET cc_start: 0.9339 (tpp) cc_final: 0.9100 (mmm) REVERT: C 123 MET cc_start: 0.9003 (mmm) cc_final: 0.8792 (mmm) REVERT: C 132 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8388 (tmm) REVERT: C 176 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8649 (mtt) REVERT: D 44 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7633 (mpp) REVERT: D 123 MET cc_start: 0.9347 (mmt) cc_final: 0.8914 (mmt) REVERT: D 132 MET cc_start: 0.8765 (tmm) cc_final: 0.8387 (ppp) REVERT: E 355 MET cc_start: 0.9105 (mtm) cc_final: 0.8797 (mmp) REVERT: W 47 PHE cc_start: 0.9602 (t80) cc_final: 0.9103 (t80) REVERT: W 72 HIS cc_start: 0.9292 (OUTLIER) cc_final: 0.9072 (t-170) REVERT: W 75 MET cc_start: 0.8342 (ptm) cc_final: 0.7947 (ptm) REVERT: W 77 HIS cc_start: 0.9585 (t70) cc_final: 0.9299 (t-90) REVERT: W 84 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8642 (ptm160) REVERT: W 127 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8795 (pt) REVERT: W 129 ASN cc_start: 0.8638 (t0) cc_final: 0.8379 (t0) REVERT: W 139 GLN cc_start: 0.8987 (mp10) cc_final: 0.8421 (mp10) REVERT: W 153 TYR cc_start: 0.8766 (t80) cc_final: 0.8024 (t80) REVERT: W 157 MET cc_start: 0.9272 (mmp) cc_final: 0.8350 (mmp) REVERT: W 179 HIS cc_start: 0.9365 (m90) cc_final: 0.9058 (m-70) REVERT: W 182 TRP cc_start: 0.8948 (t-100) cc_final: 0.8596 (t-100) REVERT: W 196 TYR cc_start: 0.9458 (t80) cc_final: 0.9244 (t80) REVERT: W 197 ILE cc_start: 0.9630 (mm) cc_final: 0.9302 (tp) REVERT: X 118 PHE cc_start: 0.9398 (t80) cc_final: 0.9051 (t80) REVERT: X 146 MET cc_start: 0.7211 (ptt) cc_final: 0.6741 (pmm) REVERT: X 153 TYR cc_start: 0.9517 (t80) cc_final: 0.9271 (t80) REVERT: X 157 MET cc_start: 0.7884 (mmm) cc_final: 0.5618 (mmm) REVERT: X 194 GLN cc_start: 0.8884 (mt0) cc_final: 0.8659 (mm110) outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 0.1286 time to fit residues: 34.4687 Evaluate side-chains 176 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain W residue 72 HIS Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 72 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 77 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 173 HIS W 111 GLN X 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.039163 restraints weight = 133372.029| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.70 r_work: 0.2796 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17738 Z= 0.297 Angle : 0.705 13.921 24065 Z= 0.344 Chirality : 0.047 0.181 2673 Planarity : 0.004 0.050 3067 Dihedral : 7.643 159.174 2449 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.03 % Allowed : 7.93 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 2170 helix: 0.95 (0.17), residues: 1076 sheet: 0.36 (0.30), residues: 305 loop : -0.20 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 256 TYR 0.022 0.002 TYR X 196 PHE 0.023 0.002 PHE X 200 TRP 0.016 0.002 TRP X 143 HIS 0.011 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00659 (17738) covalent geometry : angle 0.70495 (24065) hydrogen bonds : bond 0.03203 ( 887) hydrogen bonds : angle 4.58812 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9114 (tpp) cc_final: 0.8909 (tpp) REVERT: A 132 MET cc_start: 0.8594 (tpp) cc_final: 0.7828 (tpp) REVERT: A 227 MET cc_start: 0.9423 (mmm) cc_final: 0.9163 (mmm) REVERT: A 269 MET cc_start: 0.9209 (mtm) cc_final: 0.8600 (mtm) REVERT: A 355 MET cc_start: 0.8976 (pmm) cc_final: 0.8725 (pmm) REVERT: B 40 HIS cc_start: 0.8436 (m90) cc_final: 0.8085 (m-70) REVERT: B 44 MET cc_start: 0.4676 (tmm) cc_final: 0.4249 (tmm) REVERT: B 132 MET cc_start: 0.8261 (tmm) cc_final: 0.7645 (tmm) REVERT: C 44 MET cc_start: 0.9374 (tpp) cc_final: 0.9063 (mmm) REVERT: C 176 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8661 (mtt) REVERT: C 325 MET cc_start: 0.8601 (mmm) cc_final: 0.8378 (mmm) REVERT: D 44 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.7686 (mpp) REVERT: D 123 MET cc_start: 0.9404 (mmt) cc_final: 0.9015 (mmt) REVERT: E 283 MET cc_start: 0.9174 (mmt) cc_final: 0.8622 (mpp) REVERT: E 355 MET cc_start: 0.9135 (mtm) cc_final: 0.8829 (mmp) REVERT: W 47 PHE cc_start: 0.9604 (t80) cc_final: 0.9146 (t80) REVERT: W 77 HIS cc_start: 0.9584 (t70) cc_final: 0.9356 (t-90) REVERT: W 127 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8752 (pt) REVERT: W 129 ASN cc_start: 0.8597 (t0) cc_final: 0.8352 (t0) REVERT: W 153 TYR cc_start: 0.8632 (t80) cc_final: 0.8067 (t80) REVERT: W 157 MET cc_start: 0.9139 (mmp) cc_final: 0.8530 (mmp) REVERT: W 179 HIS cc_start: 0.9377 (m90) cc_final: 0.8956 (m90) REVERT: W 182 TRP cc_start: 0.8971 (t-100) cc_final: 0.8561 (t-100) REVERT: W 196 TYR cc_start: 0.9468 (t80) cc_final: 0.9206 (t80) REVERT: W 197 ILE cc_start: 0.9645 (mm) cc_final: 0.9319 (tp) REVERT: X 75 MET cc_start: 0.8160 (tpt) cc_final: 0.7911 (tpt) REVERT: X 118 PHE cc_start: 0.9380 (t80) cc_final: 0.9077 (t80) REVERT: X 146 MET cc_start: 0.7173 (ptt) cc_final: 0.6366 (pmm) REVERT: X 194 GLN cc_start: 0.8879 (mt0) cc_final: 0.8618 (mm110) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1214 time to fit residues: 32.2986 Evaluate side-chains 173 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 159 ASP Chi-restraints excluded: chain W residue 167 ARG Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 45 GLN Chi-restraints excluded: chain X residue 143 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 206 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 297 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 194 GLN ** 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 = 0.3474 r_free = 0.3474 target = 0.050447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.039961 restraints weight = 129958.482| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.66 r_work: 0.2861 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17738 Z= 0.114 Angle : 0.634 15.170 24065 Z= 0.304 Chirality : 0.044 0.182 2673 Planarity : 0.004 0.125 3067 Dihedral : 7.389 146.834 2449 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.70 % Allowed : 8.36 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2170 helix: 0.99 (0.17), residues: 1083 sheet: 0.47 (0.30), residues: 299 loop : 0.00 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 119 TYR 0.019 0.001 TYR W 43 PHE 0.032 0.001 PHE X 200 TRP 0.019 0.001 TRP X 143 HIS 0.010 0.001 HIS W 72 Details of bonding type rmsd covalent geometry : bond 0.00254 (17738) covalent geometry : angle 0.63350 (24065) hydrogen bonds : bond 0.02787 ( 887) hydrogen bonds : angle 4.41772 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9414 (mmm) cc_final: 0.9160 (mmm) REVERT: A 269 MET cc_start: 0.9199 (mtm) cc_final: 0.8599 (mtm) REVERT: A 305 MET cc_start: 0.8790 (mmm) cc_final: 0.8307 (mpp) REVERT: A 355 MET cc_start: 0.8867 (pmm) cc_final: 0.8609 (pmm) REVERT: B 40 HIS cc_start: 0.8383 (m90) cc_final: 0.8058 (m90) REVERT: B 44 MET cc_start: 0.4539 (tmm) cc_final: 0.4049 (tmm) REVERT: B 132 MET cc_start: 0.8048 (tmm) cc_final: 0.7592 (tmm) REVERT: C 44 MET cc_start: 0.9349 (tpp) cc_final: 0.9087 (mmm) REVERT: C 132 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8433 (tmm) REVERT: C 176 MET cc_start: 0.8930 (mtt) cc_final: 0.8627 (mtt) REVERT: C 325 MET cc_start: 0.8489 (mmm) cc_final: 0.8247 (mmm) REVERT: D 44 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7718 (mpp) REVERT: D 123 MET cc_start: 0.9389 (mmt) cc_final: 0.8954 (mmt) REVERT: E 283 MET cc_start: 0.9114 (mmt) cc_final: 0.8621 (mpp) REVERT: E 355 MET cc_start: 0.9070 (mtm) cc_final: 0.8780 (mmp) REVERT: W 47 PHE cc_start: 0.9598 (t80) cc_final: 0.9095 (t80) REVERT: W 75 MET cc_start: 0.8368 (ptm) cc_final: 0.8003 (ptm) REVERT: W 77 HIS cc_start: 0.9584 (t70) cc_final: 0.9298 (t-90) REVERT: W 84 ARG cc_start: 0.9055 (ptm-80) cc_final: 0.8623 (ptm160) REVERT: W 127 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8877 (pt) REVERT: W 129 ASN cc_start: 0.8633 (t0) cc_final: 0.8344 (t0) REVERT: W 153 TYR cc_start: 0.8681 (t80) cc_final: 0.8275 (t80) REVERT: W 157 MET cc_start: 0.9112 (mmp) cc_final: 0.8722 (mmm) REVERT: W 179 HIS cc_start: 0.9371 (m90) cc_final: 0.8952 (m90) REVERT: W 182 TRP cc_start: 0.8980 (t-100) cc_final: 0.8546 (t-100) REVERT: W 197 ILE cc_start: 0.9619 (mm) cc_final: 0.9280 (tp) REVERT: X 75 MET cc_start: 0.8061 (tpt) cc_final: 0.7800 (tpt) REVERT: X 118 PHE cc_start: 0.9359 (t80) cc_final: 0.9027 (t80) REVERT: X 146 MET cc_start: 0.7159 (ptt) cc_final: 0.6533 (pmm) REVERT: X 194 GLN cc_start: 0.8829 (mt0) cc_final: 0.8622 (mm110) outliers start: 13 outliers final: 9 residues processed: 169 average time/residue: 0.1190 time to fit residues: 32.1417 Evaluate side-chains 172 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain W residue 127 LEU Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 68 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 39 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 0.0170 chunk 126 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** W 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN ** X 194 GLN ** 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 = 0.3470 r_free = 0.3470 target = 0.050686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040156 restraints weight = 130607.840| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.72 r_work: 0.2854 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.119 Angle : 0.634 14.779 24065 Z= 0.303 Chirality : 0.044 0.181 2673 Planarity : 0.004 0.048 3067 Dihedral : 7.134 133.474 2449 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.76 % Allowed : 8.63 % Favored : 90.61 % 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: 0.81 (0.19), residues: 2170 helix: 1.03 (0.17), residues: 1083 sheet: 0.50 (0.30), residues: 309 loop : 0.02 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 119 TYR 0.039 0.001 TYR X 153 PHE 0.029 0.001 PHE X 200 TRP 0.012 0.001 TRP X 182 HIS 0.010 0.001 HIS X 77 Details of bonding type rmsd covalent geometry : bond 0.00270 (17738) covalent geometry : angle 0.63397 (24065) hydrogen bonds : bond 0.02732 ( 887) hydrogen bonds : angle 4.37845 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4264.44 seconds wall clock time: 73 minutes 44.73 seconds (4424.73 seconds total)