Starting phenix.real_space_refine on Tue May 13 21:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0y_61062/05_2025/9j0y_61062.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 52 5.16 5 C 7244 2.51 5 N 1812 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10936 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2732 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2734 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2732 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2734 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.87, per 1000 atoms: 0.72 Number of scatterers: 10936 At special positions: 0 Unit cell: (99.6, 111.22, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 52 16.00 O 1824 8.00 N 1812 7.00 C 7244 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 6 sheets defined 65.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.771A pdb=" N MET A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.700A pdb=" N TRP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 4.058A pdb=" N MET A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.519A pdb=" N GLN A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.659A pdb=" N LEU A 170 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.521A pdb=" N LEU A 175 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 176 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.943A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 225 removed outlier: 3.591A pdb=" N GLU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.900A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.661A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.562A pdb=" N PHE A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.767A pdb=" N ILE A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 4.003A pdb=" N PHE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.783A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.783A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.767A pdb=" N TYR B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.585A pdb=" N PHE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.973A pdb=" N ASP B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.535A pdb=" N LYS B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.529A pdb=" N LEU B 170 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 173 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.654A pdb=" N PHE B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 201 through 225 removed outlier: 3.702A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.931A pdb=" N TYR B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 311 removed outlier: 3.503A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.702A pdb=" N ARG B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.819A pdb=" N GLN B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.737A pdb=" N MET C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.571A pdb=" N VAL C 74 " --> pdb=" O PHE C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.928A pdb=" N THR C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 103 removed outlier: 3.559A pdb=" N ILE C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.589A pdb=" N VAL C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.945A pdb=" N PHE C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.687A pdb=" N PHE C 152 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.666A pdb=" N TYR C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.684A pdb=" N VAL C 167 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 171 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 176 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.804A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 225 removed outlier: 3.850A pdb=" N ILE C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 217 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.556A pdb=" N PHE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 311 removed outlier: 3.647A pdb=" N VAL C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.690A pdb=" N ARG C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 358 through 363 removed outlier: 4.184A pdb=" N GLN C 362 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 363 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 376 removed outlier: 4.029A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 4.044A pdb=" N SER D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.515A pdb=" N PHE D 89 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.205A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.594A pdb=" N TRP D 172 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 173 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 4.282A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 225 removed outlier: 3.578A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D 217 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 282 through 312 removed outlier: 3.552A pdb=" N SER D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 331 removed outlier: 3.779A pdb=" N ASN D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.527A pdb=" N GLY D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL D 347 " --> pdb=" O ILE D 343 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG D 348 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 removed outlier: 3.866A pdb=" N LYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 removed outlier: 3.640A pdb=" N TYR A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 241 removed outlier: 3.727A pdb=" N TYR B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.958A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 240 through 241 437 hydrogen bonds defined for protein. 1188 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: 2.73 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3211 1.34 - 1.46: 2460 1.46 - 1.57: 5476 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 11240 Sorted by residual: bond pdb=" C ILE B 364 " pdb=" N PRO B 365 " ideal model delta sigma weight residual 1.331 1.370 -0.038 1.21e-02 6.83e+03 1.00e+01 bond pdb=" CB ASP B 352 " pdb=" CG ASP B 352 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.24e+00 bond pdb=" CA THR D 356 " pdb=" C THR D 356 " ideal model delta sigma weight residual 1.522 1.554 -0.031 1.37e-02 5.33e+03 5.21e+00 bond pdb=" CA ASP B 352 " pdb=" CB ASP B 352 " ideal model delta sigma weight residual 1.541 1.564 -0.023 1.20e-02 6.94e+03 3.60e+00 bond pdb=" CB THR B 212 " pdb=" CG2 THR B 212 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 ... (remaining 11235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14737 2.41 - 4.82: 411 4.82 - 7.24: 52 7.24 - 9.65: 16 9.65 - 12.06: 4 Bond angle restraints: 15220 Sorted by residual: angle pdb=" N VAL D 347 " pdb=" CA VAL D 347 " pdb=" C VAL D 347 " ideal model delta sigma weight residual 111.77 105.27 6.50 1.04e+00 9.25e-01 3.91e+01 angle pdb=" N THR D 199 " pdb=" CA THR D 199 " pdb=" C THR D 199 " ideal model delta sigma weight residual 114.09 106.83 7.26 1.55e+00 4.16e-01 2.20e+01 angle pdb=" N ILE D 135 " pdb=" CA ILE D 135 " pdb=" C ILE D 135 " ideal model delta sigma weight residual 113.39 106.58 6.81 1.47e+00 4.63e-01 2.15e+01 angle pdb=" C TYR B 351 " pdb=" N ASP B 352 " pdb=" CA ASP B 352 " ideal model delta sigma weight residual 126.45 134.60 -8.15 1.77e+00 3.19e-01 2.12e+01 angle pdb=" C LEU C 339 " pdb=" N ARG C 340 " pdb=" CA ARG C 340 " ideal model delta sigma weight residual 120.38 126.99 -6.61 1.46e+00 4.69e-01 2.05e+01 ... (remaining 15215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 5534 15.37 - 30.74: 777 30.74 - 46.12: 192 46.12 - 61.49: 29 61.49 - 76.86: 4 Dihedral angle restraints: 6536 sinusoidal: 2664 harmonic: 3872 Sorted by residual: dihedral pdb=" CA ASP A 363 " pdb=" C ASP A 363 " pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE C 264 " pdb=" C PHE C 264 " pdb=" N ALA C 265 " pdb=" CA ALA C 265 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA SER D 161 " pdb=" C SER D 161 " pdb=" N GLY D 162 " pdb=" CA GLY D 162 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 6533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 960 0.044 - 0.087: 516 0.087 - 0.131: 137 0.131 - 0.175: 42 0.175 - 0.218: 5 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CB ILE C 236 " pdb=" CA ILE C 236 " pdb=" CG1 ILE C 236 " pdb=" CG2 ILE C 236 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 194 " pdb=" CA ILE A 194 " pdb=" CG1 ILE A 194 " pdb=" CG2 ILE A 194 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB ILE A 236 " pdb=" CA ILE A 236 " pdb=" CG1 ILE A 236 " pdb=" CG2 ILE A 236 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 1657 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 93 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO B 94 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 364 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO C 365 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 365 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 365 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 364 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 365 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.030 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 10 2.31 - 3.01: 5440 3.01 - 3.72: 18864 3.72 - 4.43: 29752 4.43 - 5.14: 49348 Nonbonded interactions: 103414 Sorted by model distance: nonbonded pdb=" OE1 GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 1.596 3.120 nonbonded pdb=" CD GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 2.129 3.350 nonbonded pdb=" OE2 GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 2.189 3.120 nonbonded pdb=" O LEU B 349 " pdb=" OG SER B 353 " model vdw 2.236 3.040 nonbonded pdb=" O ASP A 352 " pdb=" OG1 THR A 356 " model vdw 2.261 3.040 ... (remaining 103409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 52 through 376) selection = (chain 'B' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 376)) selection = chain 'C' selection = (chain 'D' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 376)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.930 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.006 0.062 11240 Z= 0.283 Angle : 0.986 12.060 15220 Z= 0.561 Chirality : 0.056 0.218 1660 Planarity : 0.006 0.061 1860 Dihedral : 14.826 76.861 4056 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.17), residues: 1292 helix: -3.90 (0.11), residues: 799 sheet: -4.04 (1.21), residues: 10 loop : -2.53 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 255 HIS 0.014 0.001 HIS C 354 PHE 0.030 0.002 PHE C 264 TYR 0.028 0.002 TYR D 351 ARG 0.010 0.001 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.25004 ( 437) hydrogen bonds : angle 8.31461 ( 1188) covalent geometry : bond 0.00622 (11240) covalent geometry : angle 0.98568 (15220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.7919 (mm) cc_final: 0.7706 (mp) REVERT: A 121 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.6594 (tpp-160) REVERT: A 166 LEU cc_start: 0.8777 (tt) cc_final: 0.8487 (tp) REVERT: A 196 TYR cc_start: 0.8112 (t80) cc_final: 0.7550 (t80) REVERT: A 323 MET cc_start: 0.5615 (ttm) cc_final: 0.5235 (ptt) REVERT: B 166 LEU cc_start: 0.8378 (tt) cc_final: 0.8140 (mm) REVERT: B 322 LYS cc_start: 0.8569 (mmpt) cc_final: 0.7833 (mttp) REVERT: C 166 LEU cc_start: 0.8416 (tt) cc_final: 0.8160 (mm) REVERT: C 204 LEU cc_start: 0.8472 (mm) cc_final: 0.8120 (mm) REVERT: C 210 TYR cc_start: 0.8492 (t80) cc_final: 0.8270 (t80) REVERT: C 269 MET cc_start: 0.8911 (tmm) cc_final: 0.8625 (ttp) REVERT: D 155 ASP cc_start: 0.7736 (t70) cc_final: 0.7469 (t0) REVERT: D 329 PHE cc_start: 0.6065 (t80) cc_final: 0.5757 (t80) REVERT: D 374 GLN cc_start: 0.5646 (mp-120) cc_final: 0.5236 (pt0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2928 time to fit residues: 88.3116 Evaluate side-chains 159 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 186 GLN A 354 HIS B 143 HIS B 230 ASN C 115 GLN ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 230 ASN D 342 GLN D 346 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115576 restraints weight = 14343.558| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.07 r_work: 0.3138 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11240 Z= 0.155 Angle : 0.653 9.043 15220 Z= 0.352 Chirality : 0.043 0.152 1660 Planarity : 0.005 0.051 1860 Dihedral : 6.464 33.715 1488 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.72 % Allowed : 10.52 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.20), residues: 1292 helix: -2.66 (0.15), residues: 814 sheet: -3.57 (1.27), residues: 10 loop : -1.85 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 255 HIS 0.004 0.001 HIS A 213 PHE 0.036 0.001 PHE C 264 TYR 0.013 0.001 TYR A 263 ARG 0.004 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05627 ( 437) hydrogen bonds : angle 5.09661 ( 1188) covalent geometry : bond 0.00344 (11240) covalent geometry : angle 0.65329 (15220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 121 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.6866 (tpp-160) REVERT: A 196 TYR cc_start: 0.8231 (t80) cc_final: 0.7689 (t80) REVERT: A 289 MET cc_start: 0.9016 (mtp) cc_final: 0.8747 (mtp) REVERT: A 309 LEU cc_start: 0.8345 (mp) cc_final: 0.8119 (mm) REVERT: A 323 MET cc_start: 0.5763 (ttm) cc_final: 0.5360 (ptt) REVERT: B 127 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7000 (ttt90) REVERT: B 146 MET cc_start: 0.8499 (ptt) cc_final: 0.8248 (ptt) REVERT: B 322 LYS cc_start: 0.8606 (mmpt) cc_final: 0.8099 (mttp) REVERT: C 115 GLN cc_start: 0.7906 (mt0) cc_final: 0.7668 (mt0) REVERT: C 166 LEU cc_start: 0.8549 (tt) cc_final: 0.8187 (mm) REVERT: C 282 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 320 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7727 (mtp85) REVERT: D 130 TYR cc_start: 0.7603 (m-80) cc_final: 0.6979 (m-80) REVERT: D 134 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7274 (mtp-110) REVERT: D 155 ASP cc_start: 0.8087 (t70) cc_final: 0.7854 (t0) REVERT: D 329 PHE cc_start: 0.6215 (t80) cc_final: 0.5815 (t80) REVERT: D 360 MET cc_start: 0.5739 (mmp) cc_final: 0.3843 (mtt) REVERT: D 374 GLN cc_start: 0.5598 (mp-120) cc_final: 0.5187 (pt0) outliers start: 20 outliers final: 8 residues processed: 198 average time/residue: 0.2640 time to fit residues: 70.7892 Evaluate side-chains 168 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 123 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118257 restraints weight = 14400.163| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.93 r_work: 0.3186 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11240 Z= 0.112 Angle : 0.571 8.155 15220 Z= 0.310 Chirality : 0.041 0.157 1660 Planarity : 0.004 0.045 1860 Dihedral : 5.819 29.547 1488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.07 % Allowed : 12.59 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.22), residues: 1292 helix: -1.85 (0.17), residues: 813 sheet: -3.25 (1.34), residues: 10 loop : -1.43 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 255 HIS 0.018 0.001 HIS D 59 PHE 0.015 0.001 PHE B 319 TYR 0.020 0.001 TYR B 196 ARG 0.004 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 437) hydrogen bonds : angle 4.47653 ( 1188) covalent geometry : bond 0.00238 (11240) covalent geometry : angle 0.57101 (15220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 117 PHE cc_start: 0.8114 (m-10) cc_final: 0.7858 (m-10) REVERT: A 121 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.6923 (tpp-160) REVERT: A 196 TYR cc_start: 0.8201 (t80) cc_final: 0.7691 (t80) REVERT: A 289 MET cc_start: 0.8972 (mtp) cc_final: 0.8609 (mtp) REVERT: A 309 LEU cc_start: 0.8345 (mp) cc_final: 0.8099 (mm) REVERT: B 124 GLN cc_start: 0.7941 (mt0) cc_final: 0.7589 (mp10) REVERT: B 127 ARG cc_start: 0.7724 (mtp-110) cc_final: 0.7233 (ttt90) REVERT: B 193 ARG cc_start: 0.6619 (mtp-110) cc_final: 0.6273 (mtm180) REVERT: B 322 LYS cc_start: 0.8594 (mmpt) cc_final: 0.7959 (mttp) REVERT: B 330 MET cc_start: 0.6619 (ttt) cc_final: 0.6237 (ttt) REVERT: C 282 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8616 (mp) REVERT: D 113 VAL cc_start: 0.7937 (t) cc_final: 0.7712 (m) REVERT: D 130 TYR cc_start: 0.7511 (m-80) cc_final: 0.7309 (m-10) REVERT: D 329 PHE cc_start: 0.6201 (t80) cc_final: 0.5761 (t80) REVERT: D 374 GLN cc_start: 0.5600 (mp-120) cc_final: 0.5383 (pt0) outliers start: 24 outliers final: 9 residues processed: 200 average time/residue: 0.2529 time to fit residues: 69.5035 Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS B 115 GLN B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 115 GLN D 248 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118694 restraints weight = 14293.224| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.84 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11240 Z= 0.111 Angle : 0.567 10.360 15220 Z= 0.301 Chirality : 0.041 0.167 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.488 26.694 1488 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.90 % Allowed : 14.48 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1292 helix: -1.41 (0.18), residues: 804 sheet: -2.94 (1.45), residues: 10 loop : -1.16 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.002 0.001 HIS B 213 PHE 0.027 0.001 PHE C 264 TYR 0.017 0.001 TYR B 196 ARG 0.003 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 437) hydrogen bonds : angle 4.20442 ( 1188) covalent geometry : bond 0.00242 (11240) covalent geometry : angle 0.56698 (15220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8150 (tt) REVERT: A 121 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.6916 (tpp-160) REVERT: A 289 MET cc_start: 0.8908 (mtp) cc_final: 0.8576 (mtp) REVERT: A 309 LEU cc_start: 0.8353 (mp) cc_final: 0.8101 (mm) REVERT: B 124 GLN cc_start: 0.7938 (mt0) cc_final: 0.7512 (mp10) REVERT: B 166 LEU cc_start: 0.8601 (tt) cc_final: 0.8248 (mm) REVERT: B 322 LYS cc_start: 0.8557 (mmpt) cc_final: 0.8093 (mttp) REVERT: C 166 LEU cc_start: 0.8459 (tt) cc_final: 0.8156 (mm) REVERT: C 282 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8625 (mp) REVERT: D 127 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7207 (mmm160) REVERT: D 165 GLU cc_start: 0.8516 (tp30) cc_final: 0.8225 (tp30) REVERT: D 329 PHE cc_start: 0.6179 (t80) cc_final: 0.5751 (t80) REVERT: D 356 THR cc_start: 0.5279 (OUTLIER) cc_final: 0.4707 (m) REVERT: D 360 MET cc_start: 0.5877 (mmp) cc_final: 0.3884 (mtt) outliers start: 22 outliers final: 10 residues processed: 188 average time/residue: 0.2371 time to fit residues: 62.1122 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 356 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 120 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS C 115 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119100 restraints weight = 14240.493| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.11 r_work: 0.3163 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11240 Z= 0.130 Angle : 0.575 8.450 15220 Z= 0.306 Chirality : 0.042 0.170 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.322 26.429 1488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.41 % Allowed : 15.09 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.23), residues: 1292 helix: -1.19 (0.18), residues: 808 sheet: -2.59 (1.56), residues: 10 loop : -0.91 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.001 PHE C 264 TYR 0.020 0.001 TYR D 130 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 437) hydrogen bonds : angle 4.07457 ( 1188) covalent geometry : bond 0.00293 (11240) covalent geometry : angle 0.57476 (15220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 114 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 121 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.6864 (tpp-160) REVERT: A 289 MET cc_start: 0.9023 (mtp) cc_final: 0.8697 (mtp) REVERT: A 309 LEU cc_start: 0.8381 (mp) cc_final: 0.8102 (mm) REVERT: B 124 GLN cc_start: 0.7864 (mt0) cc_final: 0.7452 (mp10) REVERT: B 146 MET cc_start: 0.8466 (ptt) cc_final: 0.8156 (ptt) REVERT: B 322 LYS cc_start: 0.8584 (mmpt) cc_final: 0.8168 (mttp) REVERT: C 63 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7081 (tmt170) REVERT: C 166 LEU cc_start: 0.8478 (tt) cc_final: 0.8139 (mm) REVERT: C 282 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8713 (mp) REVERT: D 113 VAL cc_start: 0.7946 (t) cc_final: 0.7680 (m) REVERT: D 130 TYR cc_start: 0.7541 (m-10) cc_final: 0.7149 (m-10) REVERT: D 165 GLU cc_start: 0.8464 (tp30) cc_final: 0.8199 (tp30) REVERT: D 319 PHE cc_start: 0.8336 (t80) cc_final: 0.8122 (t80) REVERT: D 329 PHE cc_start: 0.6248 (t80) cc_final: 0.5848 (t80) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.2488 time to fit residues: 65.1817 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS C 115 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116060 restraints weight = 14285.531| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.86 r_work: 0.3182 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11240 Z= 0.126 Angle : 0.582 9.080 15220 Z= 0.306 Chirality : 0.042 0.165 1660 Planarity : 0.003 0.041 1860 Dihedral : 5.234 26.604 1488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.84 % Allowed : 15.00 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1292 helix: -1.04 (0.18), residues: 807 sheet: -1.89 (1.26), residues: 20 loop : -0.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.012 0.001 HIS D 59 PHE 0.012 0.001 PHE C 264 TYR 0.014 0.001 TYR B 196 ARG 0.003 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 437) hydrogen bonds : angle 4.02384 ( 1188) covalent geometry : bond 0.00285 (11240) covalent geometry : angle 0.58198 (15220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 114 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8080 (tt) REVERT: A 289 MET cc_start: 0.8990 (mtp) cc_final: 0.8652 (mtp) REVERT: B 66 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7633 (mmtm) REVERT: B 124 GLN cc_start: 0.7925 (mt0) cc_final: 0.7500 (mp10) REVERT: B 146 MET cc_start: 0.8482 (ptt) cc_final: 0.8208 (ptt) REVERT: B 322 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8281 (mttp) REVERT: C 121 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7337 (tmt170) REVERT: C 166 LEU cc_start: 0.8443 (tt) cc_final: 0.8106 (mm) REVERT: C 282 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 113 VAL cc_start: 0.7865 (t) cc_final: 0.7599 (m) REVERT: D 127 ARG cc_start: 0.7298 (mmm160) cc_final: 0.7079 (mmm160) REVERT: D 130 TYR cc_start: 0.7564 (m-10) cc_final: 0.7145 (m-10) REVERT: D 165 GLU cc_start: 0.8382 (tp30) cc_final: 0.8131 (tp30) REVERT: D 296 MET cc_start: 0.8674 (ttp) cc_final: 0.8337 (ttp) REVERT: D 319 PHE cc_start: 0.8309 (t80) cc_final: 0.8083 (t80) REVERT: D 329 PHE cc_start: 0.6294 (t80) cc_final: 0.5905 (t80) REVERT: D 360 MET cc_start: 0.5992 (mmp) cc_final: 0.4049 (mtp) outliers start: 33 outliers final: 20 residues processed: 187 average time/residue: 0.2484 time to fit residues: 64.5198 Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 77 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS C 115 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123334 restraints weight = 14439.267| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.34 r_work: 0.3185 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11240 Z= 0.106 Angle : 0.552 9.332 15220 Z= 0.291 Chirality : 0.041 0.158 1660 Planarity : 0.003 0.040 1860 Dihedral : 5.058 27.348 1488 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.07 % Allowed : 16.38 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.24), residues: 1292 helix: -0.82 (0.18), residues: 814 sheet: -1.86 (1.24), residues: 20 loop : -0.59 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.002 0.000 HIS B 213 PHE 0.013 0.001 PHE C 264 TYR 0.013 0.001 TYR B 196 ARG 0.004 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 437) hydrogen bonds : angle 3.87320 ( 1188) covalent geometry : bond 0.00229 (11240) covalent geometry : angle 0.55240 (15220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7869 (t0) cc_final: 0.7479 (t0) REVERT: A 86 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 114 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 121 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7223 (tpp80) REVERT: A 289 MET cc_start: 0.9004 (mtp) cc_final: 0.8660 (mtp) REVERT: B 124 GLN cc_start: 0.7909 (mt0) cc_final: 0.7449 (mp10) REVERT: B 322 LYS cc_start: 0.8509 (mmpt) cc_final: 0.8217 (mttp) REVERT: C 115 GLN cc_start: 0.8085 (mt0) cc_final: 0.7866 (mt0) REVERT: C 166 LEU cc_start: 0.8453 (tt) cc_final: 0.8137 (mm) REVERT: C 282 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (mp) REVERT: C 354 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.5499 (p-80) REVERT: D 113 VAL cc_start: 0.7797 (t) cc_final: 0.7521 (m) REVERT: D 130 TYR cc_start: 0.7548 (m-10) cc_final: 0.7078 (m-10) REVERT: D 165 GLU cc_start: 0.8352 (tp30) cc_final: 0.8110 (tp30) REVERT: D 319 PHE cc_start: 0.8281 (t80) cc_final: 0.8044 (t80) REVERT: D 329 PHE cc_start: 0.6375 (t80) cc_final: 0.5974 (t80) outliers start: 24 outliers final: 14 residues processed: 194 average time/residue: 0.2339 time to fit residues: 63.1279 Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS D 59 HIS D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117297 restraints weight = 14147.823| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.82 r_work: 0.3193 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11240 Z= 0.123 Angle : 0.593 12.567 15220 Z= 0.306 Chirality : 0.042 0.156 1660 Planarity : 0.003 0.040 1860 Dihedral : 5.019 26.879 1488 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.16 % Allowed : 17.67 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1292 helix: -0.71 (0.18), residues: 813 sheet: -1.86 (1.21), residues: 20 loop : -0.51 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.005 0.001 HIS D 59 PHE 0.012 0.001 PHE D 198 TYR 0.013 0.001 TYR B 196 ARG 0.004 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 437) hydrogen bonds : angle 3.92183 ( 1188) covalent geometry : bond 0.00278 (11240) covalent geometry : angle 0.59325 (15220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7923 (t0) cc_final: 0.7652 (t0) REVERT: A 114 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 121 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.7258 (tpp80) REVERT: A 289 MET cc_start: 0.8899 (mtp) cc_final: 0.8569 (mtp) REVERT: B 124 GLN cc_start: 0.7853 (mt0) cc_final: 0.7443 (mp10) REVERT: B 166 LEU cc_start: 0.8413 (tt) cc_final: 0.8077 (mm) REVERT: C 131 LYS cc_start: 0.7334 (tttm) cc_final: 0.7068 (tmtt) REVERT: C 166 LEU cc_start: 0.8516 (tt) cc_final: 0.8183 (mm) REVERT: C 282 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (mp) REVERT: C 354 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.5558 (p-80) REVERT: D 113 VAL cc_start: 0.7937 (t) cc_final: 0.7681 (m) REVERT: D 130 TYR cc_start: 0.7480 (m-10) cc_final: 0.7251 (m-80) REVERT: D 146 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6294 (ppp) REVERT: D 165 GLU cc_start: 0.8249 (tp30) cc_final: 0.8007 (tp30) REVERT: D 319 PHE cc_start: 0.8326 (t80) cc_final: 0.8075 (t80) REVERT: D 329 PHE cc_start: 0.6332 (t80) cc_final: 0.5864 (t80) REVERT: D 360 MET cc_start: 0.6101 (mmp) cc_final: 0.4192 (mtt) outliers start: 25 outliers final: 15 residues processed: 186 average time/residue: 0.2526 time to fit residues: 64.6284 Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS D 59 HIS D 248 ASN D 305 ASN D 374 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119242 restraints weight = 14413.709| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.06 r_work: 0.3190 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11240 Z= 0.114 Angle : 0.592 12.198 15220 Z= 0.305 Chirality : 0.042 0.202 1660 Planarity : 0.003 0.038 1860 Dihedral : 4.973 27.340 1488 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.07 % Allowed : 17.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1292 helix: -0.54 (0.18), residues: 812 sheet: -1.77 (1.21), residues: 20 loop : -0.45 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS C 354 PHE 0.028 0.001 PHE B 319 TYR 0.014 0.001 TYR B 196 ARG 0.004 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 437) hydrogen bonds : angle 3.88454 ( 1188) covalent geometry : bond 0.00254 (11240) covalent geometry : angle 0.59199 (15220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7879 (t0) cc_final: 0.7539 (t0) REVERT: A 86 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 114 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8116 (tt) REVERT: A 121 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7202 (tpp80) REVERT: A 289 MET cc_start: 0.8968 (mtp) cc_final: 0.8630 (mtp) REVERT: B 124 GLN cc_start: 0.7883 (mt0) cc_final: 0.7429 (mp10) REVERT: B 166 LEU cc_start: 0.8408 (tt) cc_final: 0.8048 (mm) REVERT: C 131 LYS cc_start: 0.7328 (tttm) cc_final: 0.7069 (tmtt) REVERT: C 166 LEU cc_start: 0.8488 (tt) cc_final: 0.8149 (mm) REVERT: C 282 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8684 (mp) REVERT: C 354 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.5543 (p-80) REVERT: D 59 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7372 (t70) REVERT: D 130 TYR cc_start: 0.7513 (m-10) cc_final: 0.7210 (m-10) REVERT: D 146 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6414 (ppp) REVERT: D 165 GLU cc_start: 0.8294 (tp30) cc_final: 0.8061 (tp30) REVERT: D 312 LYS cc_start: 0.7756 (tppt) cc_final: 0.7320 (tttt) REVERT: D 319 PHE cc_start: 0.8299 (t80) cc_final: 0.8036 (t80) REVERT: D 329 PHE cc_start: 0.6328 (t80) cc_final: 0.5680 (t80) outliers start: 24 outliers final: 13 residues processed: 186 average time/residue: 0.2477 time to fit residues: 64.0682 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 113 optimal weight: 0.0020 chunk 100 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS C 362 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.180293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116099 restraints weight = 14275.214| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.88 r_work: 0.3184 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11240 Z= 0.131 Angle : 0.613 13.039 15220 Z= 0.317 Chirality : 0.042 0.184 1660 Planarity : 0.003 0.036 1860 Dihedral : 4.978 26.703 1488 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.98 % Allowed : 17.33 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1292 helix: -0.49 (0.19), residues: 811 sheet: -1.63 (1.24), residues: 20 loop : -0.44 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 255 HIS 0.004 0.001 HIS D 59 PHE 0.026 0.001 PHE B 319 TYR 0.016 0.001 TYR B 351 ARG 0.005 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 437) hydrogen bonds : angle 3.95400 ( 1188) covalent geometry : bond 0.00301 (11240) covalent geometry : angle 0.61263 (15220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7905 (t0) cc_final: 0.7641 (t0) REVERT: A 86 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8637 (tm-30) REVERT: A 114 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 121 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7254 (tpp80) REVERT: A 289 MET cc_start: 0.8931 (mtp) cc_final: 0.8605 (mtp) REVERT: B 124 GLN cc_start: 0.7887 (mt0) cc_final: 0.7438 (mp10) REVERT: B 166 LEU cc_start: 0.8391 (tt) cc_final: 0.8097 (mm) REVERT: C 69 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 131 LYS cc_start: 0.7352 (tttm) cc_final: 0.7119 (tmtt) REVERT: C 166 LEU cc_start: 0.8515 (tt) cc_final: 0.8189 (mm) REVERT: C 282 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (mp) REVERT: C 354 HIS cc_start: 0.6839 (OUTLIER) cc_final: 0.5612 (p-80) REVERT: D 59 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7649 (t70) REVERT: D 165 GLU cc_start: 0.8231 (tp30) cc_final: 0.8010 (tp30) REVERT: D 312 LYS cc_start: 0.7843 (tppt) cc_final: 0.7397 (tttt) REVERT: D 319 PHE cc_start: 0.8309 (t80) cc_final: 0.8046 (t80) REVERT: D 329 PHE cc_start: 0.6284 (t80) cc_final: 0.5640 (t80) outliers start: 23 outliers final: 16 residues processed: 180 average time/residue: 0.2503 time to fit residues: 62.9670 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 116 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS C 115 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.180973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120455 restraints weight = 14289.647| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.10 r_work: 0.3164 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11240 Z= 0.128 Angle : 0.617 13.444 15220 Z= 0.317 Chirality : 0.042 0.176 1660 Planarity : 0.003 0.038 1860 Dihedral : 4.942 26.921 1488 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.07 % Allowed : 17.24 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1292 helix: -0.39 (0.19), residues: 804 sheet: -1.49 (1.26), residues: 20 loop : -0.47 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 255 HIS 0.003 0.001 HIS D 59 PHE 0.024 0.001 PHE B 319 TYR 0.016 0.001 TYR B 196 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 437) hydrogen bonds : angle 3.93191 ( 1188) covalent geometry : bond 0.00291 (11240) covalent geometry : angle 0.61651 (15220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7544.65 seconds wall clock time: 130 minutes 47.78 seconds (7847.78 seconds total)