Starting phenix.real_space_refine on Mon Jun 9 21:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0y_61062/06_2025/9j0y_61062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0y_61062/06_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_61062/06_2025/9j0y_61062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0y_61062/06_2025/9j0y_61062.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0y_61062/06_2025/9j0y_61062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0y_61062/06_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-5710/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: 8.11, per 1000 atoms: 0.74 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: 2.78 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: 0.95 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: 2.69 Time building geometry restraints manager: 3.26 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: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.620 Find NCS groups from input model: 0.530 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- 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 : 1.251 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: 0.2866 time to fit residues: 86.9388 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 : 1.197 ------------------------------------------------------------------------------- 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 = 0.115574 restraints weight = 14343.558| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.07 r_work: 0.3137 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- 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 : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 121 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.6867 (tpp-160) REVERT: A 196 TYR cc_start: 0.8233 (t80) cc_final: 0.7689 (t80) REVERT: A 289 MET cc_start: 0.9020 (mtp) cc_final: 0.8753 (mtp) REVERT: A 309 LEU cc_start: 0.8345 (mp) cc_final: 0.8118 (mm) REVERT: A 323 MET cc_start: 0.5769 (ttm) cc_final: 0.5365 (ptt) REVERT: B 127 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7000 (ttt90) REVERT: B 146 MET cc_start: 0.8498 (ptt) cc_final: 0.8247 (ptt) REVERT: B 322 LYS cc_start: 0.8606 (mmpt) cc_final: 0.8099 (mttp) REVERT: C 115 GLN cc_start: 0.7908 (mt0) cc_final: 0.7670 (mt0) REVERT: C 166 LEU cc_start: 0.8550 (tt) cc_final: 0.8187 (mm) REVERT: C 282 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 320 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7730 (mtp85) REVERT: D 130 TYR cc_start: 0.7603 (m-80) cc_final: 0.6979 (m-80) REVERT: D 134 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7275 (mtp-110) REVERT: D 155 ASP cc_start: 0.8089 (t70) cc_final: 0.7854 (t0) REVERT: D 329 PHE cc_start: 0.6215 (t80) cc_final: 0.5816 (t80) REVERT: D 360 MET cc_start: 0.5740 (mmp) cc_final: 0.3843 (mtt) REVERT: D 374 GLN cc_start: 0.5599 (mp-120) cc_final: 0.5185 (pt0) outliers start: 20 outliers final: 8 residues processed: 198 average time/residue: 0.2682 time to fit residues: 72.1006 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 : 1.175 ------------------------------------------------------------------------------- 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: 0.0670 chunk 39 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 123 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0338 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.177120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114453 restraints weight = 14412.007| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.04 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11240 Z= 0.179 Angle : 0.627 7.867 15220 Z= 0.338 Chirality : 0.044 0.152 1660 Planarity : 0.004 0.046 1860 Dihedral : 6.056 29.932 1488 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.59 % Allowed : 12.16 % Favored : 85.26 % 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: -2.97 (0.22), residues: 1292 helix: -2.06 (0.17), residues: 821 sheet: -3.34 (1.33), residues: 10 loop : -1.40 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 255 HIS 0.016 0.001 HIS D 59 PHE 0.015 0.002 PHE B 319 TYR 0.019 0.001 TYR B 196 ARG 0.004 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 437) hydrogen bonds : angle 4.70558 ( 1188) covalent geometry : bond 0.00415 (11240) covalent geometry : angle 0.62737 (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 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 121 ARG cc_start: 0.7917 (tpp-160) cc_final: 0.6782 (tpp-160) REVERT: A 289 MET cc_start: 0.9029 (mtp) cc_final: 0.8726 (mtp) REVERT: A 309 LEU cc_start: 0.8391 (mp) cc_final: 0.8127 (mm) REVERT: B 124 GLN cc_start: 0.7942 (mt0) cc_final: 0.7592 (mp10) REVERT: B 127 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7195 (ttt90) REVERT: B 146 MET cc_start: 0.8523 (ptt) cc_final: 0.8229 (ptt) REVERT: B 322 LYS cc_start: 0.8584 (mmpt) cc_final: 0.7941 (mttp) REVERT: C 282 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8733 (mp) REVERT: D 113 VAL cc_start: 0.8017 (t) cc_final: 0.7799 (m) REVERT: D 155 ASP cc_start: 0.8096 (t70) cc_final: 0.7891 (t0) REVERT: D 329 PHE cc_start: 0.6185 (t80) cc_final: 0.5746 (t80) REVERT: D 374 GLN cc_start: 0.5620 (mp-120) cc_final: 0.5332 (pt0) outliers start: 30 outliers final: 17 residues processed: 185 average time/residue: 0.2666 time to fit residues: 67.8267 Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 B residue 106 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 101 ASP 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 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 115 optimal weight: 0.0470 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.180486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118374 restraints weight = 14325.220| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.93 r_work: 0.3191 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2612 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= 0.113 Angle : 0.579 8.700 15220 Z= 0.306 Chirality : 0.041 0.154 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.610 27.084 1488 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.16 % Allowed : 13.88 % Favored : 83.97 % 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: -2.30 (0.23), residues: 1292 helix: -1.51 (0.18), residues: 815 sheet: -2.93 (1.51), residues: 10 loop : -1.18 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.013 0.001 HIS D 59 PHE 0.027 0.001 PHE C 264 TYR 0.018 0.001 TYR B 196 ARG 0.003 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 437) hydrogen bonds : angle 4.26096 ( 1188) covalent geometry : bond 0.00244 (11240) covalent geometry : angle 0.57852 (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 206 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 121 ARG cc_start: 0.7916 (tpp-160) cc_final: 0.6882 (tpp-160) REVERT: A 289 MET cc_start: 0.8961 (mtp) cc_final: 0.8612 (mtp) REVERT: A 309 LEU cc_start: 0.8331 (mp) cc_final: 0.8061 (mm) REVERT: B 115 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7558 (mm-40) REVERT: B 124 GLN cc_start: 0.7912 (mt0) cc_final: 0.7509 (mp10) REVERT: B 146 MET cc_start: 0.8573 (ptt) cc_final: 0.8347 (ptt) REVERT: B 319 PHE cc_start: 0.8088 (t80) cc_final: 0.7776 (t80) REVERT: B 322 LYS cc_start: 0.8582 (mmpt) cc_final: 0.8192 (mttp) REVERT: C 166 LEU cc_start: 0.8472 (tt) cc_final: 0.8151 (mm) REVERT: C 282 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 130 TYR cc_start: 0.7765 (m-10) cc_final: 0.7331 (m-10) REVERT: D 329 PHE cc_start: 0.6265 (t80) cc_final: 0.5874 (t80) REVERT: D 356 THR cc_start: 0.5258 (OUTLIER) cc_final: 0.4696 (m) REVERT: D 360 MET cc_start: 0.5954 (mmp) cc_final: 0.4044 (mtt) outliers start: 25 outliers final: 11 residues processed: 196 average time/residue: 0.2403 time to fit residues: 65.4227 Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain A residue 297 VAL 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 282 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 LEU 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: 5.9990 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.180055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117044 restraints weight = 14226.789| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.11 r_work: 0.3161 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11240 Z= 0.126 Angle : 0.579 7.310 15220 Z= 0.308 Chirality : 0.042 0.156 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.378 26.516 1488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.67 % Allowed : 15.60 % Favored : 81.72 % 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: -1.90 (0.23), residues: 1292 helix: -1.18 (0.18), residues: 797 sheet: -2.73 (1.58), residues: 10 loop : -1.07 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.003 0.001 HIS B 213 PHE 0.024 0.001 PHE C 264 TYR 0.014 0.001 TYR B 196 ARG 0.004 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 437) hydrogen bonds : angle 4.11626 ( 1188) covalent geometry : bond 0.00284 (11240) covalent geometry : angle 0.57865 (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 198 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 114 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8177 (tt) REVERT: A 121 ARG cc_start: 0.7899 (tpp-160) cc_final: 0.6812 (tpp-160) REVERT: A 289 MET cc_start: 0.9010 (mtp) cc_final: 0.8675 (mtp) REVERT: A 309 LEU cc_start: 0.8361 (mp) cc_final: 0.8087 (mm) REVERT: B 115 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7560 (mm-40) REVERT: B 124 GLN cc_start: 0.7928 (mt0) cc_final: 0.7523 (mp10) REVERT: B 146 MET cc_start: 0.8586 (ptt) cc_final: 0.8338 (ptt) REVERT: B 322 LYS cc_start: 0.8625 (mmpt) cc_final: 0.8128 (mttp) REVERT: B 326 LEU cc_start: 0.7904 (mp) cc_final: 0.7677 (mp) REVERT: C 63 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7078 (tmt170) REVERT: C 121 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7350 (tmt170) REVERT: C 166 LEU cc_start: 0.8474 (tt) cc_final: 0.8130 (mm) REVERT: C 282 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8676 (mp) REVERT: D 127 ARG cc_start: 0.7537 (mmt90) cc_final: 0.7279 (mmm160) REVERT: D 130 TYR cc_start: 0.7745 (m-10) cc_final: 0.7290 (m-10) REVERT: D 165 GLU cc_start: 0.8452 (tp30) cc_final: 0.8212 (tp30) REVERT: D 329 PHE cc_start: 0.6302 (t80) cc_final: 0.5905 (t80) outliers start: 31 outliers final: 14 residues processed: 188 average time/residue: 0.2564 time to fit residues: 66.7150 Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain A residue 297 VAL 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 99 VAL 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 D residue 73 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 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: 1.9990 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS B 143 HIS 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 = 0.4088 r_free = 0.4088 target = 0.178451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114801 restraints weight = 14277.677| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.84 r_work: 0.3148 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2919 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= 0.143 Angle : 0.585 8.069 15220 Z= 0.310 Chirality : 0.043 0.184 1660 Planarity : 0.004 0.064 1860 Dihedral : 5.322 26.368 1488 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.59 % Allowed : 16.03 % Favored : 81.38 % 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: -1.68 (0.23), residues: 1292 helix: -1.10 (0.18), residues: 804 sheet: -2.65 (1.56), residues: 10 loop : -0.80 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 255 HIS 0.003 0.001 HIS B 213 PHE 0.016 0.001 PHE C 264 TYR 0.013 0.001 TYR A 263 ARG 0.010 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 437) hydrogen bonds : angle 4.07185 ( 1188) covalent geometry : bond 0.00329 (11240) covalent geometry : angle 0.58489 (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 190 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 114 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8412 (tt) REVERT: A 289 MET cc_start: 0.8946 (mtp) cc_final: 0.8616 (mtp) REVERT: A 309 LEU cc_start: 0.8376 (mp) cc_final: 0.8102 (mm) REVERT: B 115 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7539 (mm-40) REVERT: B 124 GLN cc_start: 0.7845 (mt0) cc_final: 0.7453 (mp10) REVERT: B 322 LYS cc_start: 0.8669 (mmpt) cc_final: 0.8240 (mttp) REVERT: C 121 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7346 (tmt170) REVERT: C 166 LEU cc_start: 0.8484 (tt) cc_final: 0.8140 (mm) REVERT: C 282 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8679 (mp) REVERT: D 113 VAL cc_start: 0.7960 (t) cc_final: 0.7706 (m) REVERT: D 127 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7306 (mmm160) REVERT: D 165 GLU cc_start: 0.8384 (tp30) cc_final: 0.8160 (tp30) REVERT: D 296 MET cc_start: 0.8707 (ttp) cc_final: 0.8378 (ttp) REVERT: D 329 PHE cc_start: 0.6299 (t80) cc_final: 0.5892 (t80) REVERT: D 360 MET cc_start: 0.6013 (mmp) cc_final: 0.4251 (mtt) outliers start: 30 outliers final: 21 residues processed: 179 average time/residue: 0.2420 time to fit residues: 60.3828 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU 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 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 320 ARG 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 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 95 optimal weight: 40.0000 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.177338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114200 restraints weight = 14432.511| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.06 r_work: 0.3127 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11240 Z= 0.162 Angle : 0.595 7.487 15220 Z= 0.316 Chirality : 0.043 0.179 1660 Planarity : 0.004 0.051 1860 Dihedral : 5.312 26.483 1488 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.93 % Allowed : 16.12 % Favored : 80.95 % 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: -1.61 (0.23), residues: 1292 helix: -1.03 (0.18), residues: 809 sheet: -2.50 (1.63), residues: 10 loop : -0.78 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.008 0.001 HIS D 59 PHE 0.015 0.001 PHE C 264 TYR 0.015 0.001 TYR A 263 ARG 0.009 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 437) hydrogen bonds : angle 4.08523 ( 1188) covalent geometry : bond 0.00377 (11240) covalent geometry : angle 0.59470 (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 197 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 114 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 121 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7225 (tpp80) REVERT: A 289 MET cc_start: 0.8995 (mtp) cc_final: 0.8678 (mtp) REVERT: A 309 LEU cc_start: 0.8404 (mp) cc_final: 0.8129 (mm) REVERT: B 124 GLN cc_start: 0.7865 (mt0) cc_final: 0.7467 (mp10) REVERT: B 146 MET cc_start: 0.8626 (ptt) cc_final: 0.8347 (ptt) REVERT: B 226 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 322 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8210 (mttp) REVERT: C 121 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7343 (tmt170) REVERT: C 166 LEU cc_start: 0.8530 (tt) cc_final: 0.8173 (mm) REVERT: C 282 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 113 VAL cc_start: 0.7937 (t) cc_final: 0.7682 (m) REVERT: D 130 TYR cc_start: 0.7622 (m-10) cc_final: 0.7353 (m-80) REVERT: D 329 PHE cc_start: 0.6325 (t80) cc_final: 0.5921 (t80) REVERT: D 360 MET cc_start: 0.5938 (mmp) cc_final: 0.4246 (mtt) outliers start: 34 outliers final: 22 residues processed: 186 average time/residue: 0.2443 time to fit residues: 63.1174 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 166 LEU Chi-restraints excluded: chain B residue 226 LEU 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 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 346 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 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 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: 0.0070 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.179144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115561 restraints weight = 14207.148| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.86 r_work: 0.3164 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3102 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= 0.132 Angle : 0.583 9.214 15220 Z= 0.308 Chirality : 0.042 0.165 1660 Planarity : 0.004 0.045 1860 Dihedral : 5.228 26.425 1488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.67 % Allowed : 16.81 % Favored : 80.52 % 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: -1.43 (0.24), residues: 1292 helix: -0.91 (0.18), residues: 811 sheet: -2.56 (1.61), residues: 10 loop : -0.68 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.007 0.001 HIS D 59 PHE 0.010 0.001 PHE C 264 TYR 0.012 0.001 TYR B 196 ARG 0.007 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 437) hydrogen bonds : angle 4.01553 ( 1188) covalent geometry : bond 0.00300 (11240) covalent geometry : angle 0.58270 (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 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 114 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 121 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7237 (tpp80) REVERT: A 289 MET cc_start: 0.8938 (mtp) cc_final: 0.8609 (mtp) REVERT: A 309 LEU cc_start: 0.8385 (mp) cc_final: 0.8112 (mm) REVERT: B 124 GLN cc_start: 0.7892 (mt0) cc_final: 0.7506 (mp10) REVERT: B 146 MET cc_start: 0.8603 (ptt) cc_final: 0.8341 (ptt) REVERT: B 226 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8154 (mp) REVERT: B 322 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8330 (mttp) REVERT: C 63 ARG cc_start: 0.7881 (tpp80) cc_final: 0.6899 (tmt170) REVERT: C 166 LEU cc_start: 0.8477 (tt) cc_final: 0.8132 (mm) REVERT: C 282 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8658 (mp) REVERT: D 113 VAL cc_start: 0.7903 (t) cc_final: 0.7655 (m) REVERT: D 127 ARG cc_start: 0.7401 (mmm160) cc_final: 0.7066 (mmm160) REVERT: D 130 TYR cc_start: 0.7555 (m-10) cc_final: 0.7313 (m-80) REVERT: D 146 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6017 (ppp) REVERT: D 329 PHE cc_start: 0.6251 (t80) cc_final: 0.5784 (t80) outliers start: 31 outliers final: 22 residues processed: 182 average time/residue: 0.2575 time to fit residues: 65.1004 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 295 ASP 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 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.178655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117282 restraints weight = 14418.922| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.02 r_work: 0.3139 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3223 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= 0.143 Angle : 0.598 10.561 15220 Z= 0.312 Chirality : 0.043 0.172 1660 Planarity : 0.004 0.042 1860 Dihedral : 5.189 26.433 1488 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.02 % Allowed : 17.16 % Favored : 79.83 % 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: -1.33 (0.24), residues: 1292 helix: -0.82 (0.18), residues: 809 sheet: -2.55 (1.63), residues: 10 loop : -0.63 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.006 0.001 HIS C 354 PHE 0.027 0.001 PHE B 319 TYR 0.014 0.001 TYR A 263 ARG 0.007 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 437) hydrogen bonds : angle 4.03995 ( 1188) covalent geometry : bond 0.00330 (11240) covalent geometry : angle 0.59794 (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 203 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 114 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 121 ARG cc_start: 0.7830 (tpp-160) cc_final: 0.7257 (tpp80) REVERT: A 289 MET cc_start: 0.8992 (mtp) cc_final: 0.8669 (mtp) REVERT: B 124 GLN cc_start: 0.7872 (mt0) cc_final: 0.7518 (mp10) REVERT: B 226 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 322 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8387 (mttp) REVERT: C 131 LYS cc_start: 0.7311 (tttm) cc_final: 0.7054 (tmtt) REVERT: C 166 LEU cc_start: 0.8496 (tt) cc_final: 0.8139 (mm) REVERT: C 282 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (mp) REVERT: D 59 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7555 (t70) REVERT: D 113 VAL cc_start: 0.7914 (t) cc_final: 0.7659 (m) REVERT: D 127 ARG cc_start: 0.7428 (mmm160) cc_final: 0.7146 (mmm160) REVERT: D 146 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6194 (ppp) REVERT: D 329 PHE cc_start: 0.6229 (t80) cc_final: 0.5577 (t80) REVERT: D 360 MET cc_start: 0.6121 (mmp) cc_final: 0.4176 (mtp) outliers start: 35 outliers final: 22 residues processed: 190 average time/residue: 0.2440 time to fit residues: 63.6841 Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 295 ASP 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 231 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 375 LEU 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 145 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS D 248 ASN D 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115684 restraints weight = 14311.740| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3333 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= 0.133 Angle : 0.603 11.466 15220 Z= 0.314 Chirality : 0.042 0.177 1660 Planarity : 0.003 0.040 1860 Dihedral : 5.166 26.478 1488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.24 % Allowed : 18.10 % Favored : 79.66 % 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: -1.14 (0.24), residues: 1292 helix: -0.63 (0.19), residues: 797 sheet: -2.43 (1.69), residues: 10 loop : -0.67 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.007 0.001 HIS D 59 PHE 0.009 0.001 PHE C 71 TYR 0.015 0.001 TYR D 130 ARG 0.006 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 437) hydrogen bonds : angle 3.99263 ( 1188) covalent geometry : bond 0.00301 (11240) covalent geometry : angle 0.60276 (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 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8014 (t0) cc_final: 0.7660 (t0) REVERT: A 86 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 114 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 121 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7280 (tpp80) REVERT: A 289 MET cc_start: 0.8946 (mtp) cc_final: 0.8625 (mtp) REVERT: B 66 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7509 (mmtm) REVERT: B 124 GLN cc_start: 0.7891 (mt0) cc_final: 0.7497 (mp10) REVERT: B 226 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 322 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8412 (mttp) REVERT: C 69 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 131 LYS cc_start: 0.7311 (tttm) cc_final: 0.7078 (tmtt) REVERT: C 166 LEU cc_start: 0.8488 (tt) cc_final: 0.8149 (mm) REVERT: C 282 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8660 (mp) REVERT: D 59 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7427 (t-90) REVERT: D 113 VAL cc_start: 0.7929 (t) cc_final: 0.7663 (m) REVERT: D 127 ARG cc_start: 0.7477 (mmm160) cc_final: 0.7217 (mmm160) REVERT: D 130 TYR cc_start: 0.7498 (m-10) cc_final: 0.7236 (m-80) REVERT: D 146 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6237 (ppp) REVERT: D 165 GLU cc_start: 0.8229 (tp30) cc_final: 0.7744 (tm-30) REVERT: D 329 PHE cc_start: 0.6180 (t80) cc_final: 0.5517 (t80) REVERT: D 360 MET cc_start: 0.6115 (mmp) cc_final: 0.4260 (mtm) outliers start: 26 outliers final: 19 residues processed: 182 average time/residue: 0.2541 time to fit residues: 63.5824 Evaluate side-chains 186 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain B residue 226 LEU 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 125 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 375 LEU 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 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.177998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114027 restraints weight = 14304.416| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.89 r_work: 0.3145 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11240 Z= 0.153 Angle : 0.618 10.990 15220 Z= 0.321 Chirality : 0.043 0.176 1660 Planarity : 0.003 0.041 1860 Dihedral : 5.171 26.455 1488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.33 % Allowed : 18.36 % Favored : 79.31 % 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: -1.16 (0.24), residues: 1292 helix: -0.71 (0.18), residues: 818 sheet: -2.36 (1.75), residues: 10 loop : -0.53 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.005 0.001 HIS C 354 PHE 0.029 0.001 PHE B 319 TYR 0.016 0.001 TYR B 196 ARG 0.006 0.000 ARG C 179 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 437) hydrogen bonds : angle 4.05541 ( 1188) covalent geometry : bond 0.00356 (11240) covalent geometry : angle 0.61775 (15220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7679.65 seconds wall clock time: 131 minutes 56.50 seconds (7916.50 seconds total)