Starting phenix.real_space_refine on Sun Aug 24 04:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xt9_10617/08_2025/6xt9_10617.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10811 2.51 5 N 2888 2.21 5 O 3127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16916 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4378 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 38, 'TRANS': 528} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3069 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 385} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3192 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5834 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 31, 'TRANS': 735} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 5, 'GLU:plan': 7, 'ASP:plan': 7, 'PHE:plan': 2, 'ASN:plan1': 5, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Time building chain proxies: 3.83, per 1000 atoms: 0.23 Number of scatterers: 16916 At special positions: 0 Unit cell: (141.24, 160.5, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3127 8.00 N 2888 7.00 C 10811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 755.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4144 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 25 sheets defined 40.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.938A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.509A pdb=" N LEU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.675A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.587A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.891A pdb=" N MET A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.944A pdb=" N ILE D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.565A pdb=" N LYS D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.658A pdb=" N GLN D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 4.004A pdb=" N GLU D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 removed outlier: 4.215A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 131 removed outlier: 3.541A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 removed outlier: 3.617A pdb=" N LEU D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.963A pdb=" N ASP D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.762A pdb=" N ILE D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 removed outlier: 4.162A pdb=" N GLU D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.598A pdb=" N LEU D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 removed outlier: 3.790A pdb=" N GLU D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.669A pdb=" N LEU D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.686A pdb=" N THR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.533A pdb=" N ASN D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 283 " --> pdb=" O CYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 300 removed outlier: 3.786A pdb=" N ILE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 296 " --> pdb=" O CYS D 292 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.857A pdb=" N TYR D 308 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.532A pdb=" N PHE D 324 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.564A pdb=" N ALA D 345 " --> pdb=" O TYR D 341 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 346 " --> pdb=" O MET D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.507A pdb=" N ARG D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.835A pdb=" N ASN D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 407 through 422 removed outlier: 4.165A pdb=" N LEU D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 422 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 3.545A pdb=" N ARG H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 removed outlier: 4.165A pdb=" N ASP H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 50 removed outlier: 3.540A pdb=" N LEU H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.510A pdb=" N TYR H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 removed outlier: 3.807A pdb=" N GLU H 193 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 210 removed outlier: 3.540A pdb=" N ALA H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP H 201 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU H 202 " --> pdb=" O THR H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 removed outlier: 3.521A pdb=" N GLY H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 243 removed outlier: 4.277A pdb=" N LYS H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA H 241 " --> pdb=" O GLN H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.605A pdb=" N PHE H 251 " --> pdb=" O MET H 247 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL H 259 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.866A pdb=" N ASN H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 277 No H-bonds generated for 'chain 'H' and resid 275 through 277' Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.671A pdb=" N LEU H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.675A pdb=" N ALA H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 315 through 318 removed outlier: 3.548A pdb=" N ALA H 318 " --> pdb=" O HIS H 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 315 through 318' Processing helix chain 'H' and resid 319 through 324 Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.602A pdb=" N TYR H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 341 " --> pdb=" O ARG H 337 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 342 " --> pdb=" O PHE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 removed outlier: 3.522A pdb=" N ASN H 354 " --> pdb=" O GLY H 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 361 " --> pdb=" O GLY H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 378 removed outlier: 4.545A pdb=" N THR H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER H 372 " --> pdb=" O MET H 368 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.280A pdb=" N ASP H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 395 " --> pdb=" O TYR H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 417 removed outlier: 3.719A pdb=" N GLN H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG H 411 " --> pdb=" O HIS H 407 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 435 removed outlier: 3.790A pdb=" N ASN H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 426 " --> pdb=" O GLU H 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 429 " --> pdb=" O ASN H 425 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU H 430 " --> pdb=" O ASN H 426 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET H 432 " --> pdb=" O ALA H 428 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS H 434 " --> pdb=" O LEU H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 449 removed outlier: 3.653A pdb=" N ALA H 442 " --> pdb=" O GLU H 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 443 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN H 445 " --> pdb=" O ARG H 441 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 449 " --> pdb=" O GLN H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 462 removed outlier: 3.549A pdb=" N ALA H 462 " --> pdb=" O HIS H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.630A pdb=" N VAL H 476 " --> pdb=" O GLN H 472 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA H 478 " --> pdb=" O SER H 474 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU H 482 " --> pdb=" O ALA H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 493 removed outlier: 3.911A pdb=" N GLN H 492 " --> pdb=" O HIS H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 504 removed outlier: 3.690A pdb=" N GLN H 500 " --> pdb=" O LYS H 496 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS H 501 " --> pdb=" O GLN H 497 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 503 " --> pdb=" O ARG H 499 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET H 504 " --> pdb=" O GLN H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.663A pdb=" N GLY I 145 " --> pdb=" O SER I 142 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL I 146 " --> pdb=" O PHE I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'I' and resid 401 through 414 removed outlier: 3.605A pdb=" N THR I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP I 410 " --> pdb=" O GLU I 406 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU I 411 " --> pdb=" O ARG I 407 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN I 412 " --> pdb=" O GLU I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 558 through 562 Processing helix chain 'I' and resid 609 through 625 removed outlier: 4.187A pdb=" N ASN I 614 " --> pdb=" O TRP I 610 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 615 " --> pdb=" O LEU I 611 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 660 removed outlier: 3.987A pdb=" N GLU I 644 " --> pdb=" O ILE I 640 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU I 647 " --> pdb=" O GLN I 643 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 648 " --> pdb=" O GLU I 644 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 650 " --> pdb=" O PHE I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 684 removed outlier: 3.553A pdb=" N GLU I 668 " --> pdb=" O GLU I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 709 removed outlier: 3.590A pdb=" N ASP I 700 " --> pdb=" O ASP I 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 701 " --> pdb=" O THR I 697 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 702 " --> pdb=" O LEU I 698 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 706 " --> pdb=" O THR I 702 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 707 " --> pdb=" O TYR I 703 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 709 " --> pdb=" O GLN I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 742 removed outlier: 3.899A pdb=" N ASN I 716 " --> pdb=" O ALA I 712 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I 717 " --> pdb=" O VAL I 713 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG I 726 " --> pdb=" O GLN I 722 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU I 737 " --> pdb=" O LEU I 733 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 739 " --> pdb=" O ILE I 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 740 " --> pdb=" O LEU I 736 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN I 742 " --> pdb=" O ILE I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 747 through 756 removed outlier: 3.605A pdb=" N ALA I 754 " --> pdb=" O ALA I 750 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 780 removed outlier: 3.830A pdb=" N ASP I 773 " --> pdb=" O GLU I 769 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 774 " --> pdb=" O GLU I 770 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS I 778 " --> pdb=" O ALA I 774 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU I 780 " --> pdb=" O ILE I 776 " (cutoff:3.500A) Processing helix chain 'I' and resid 788 through 799 removed outlier: 3.733A pdb=" N LEU I 795 " --> pdb=" O GLN I 791 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN I 798 " --> pdb=" O ASN I 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 80 removed outlier: 3.952A pdb=" N ASN J 75 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN J 79 " --> pdb=" O ASN J 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN J 80 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 removed outlier: 5.410A pdb=" N ASP A 25 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 401 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 27 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 398 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 400 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 388 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR A 381 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 375 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.646A pdb=" N ALA A 44 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 78 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 72 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 92 removed outlier: 3.664A pdb=" N ALA A 88 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 114 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 121 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 207 removed outlier: 3.689A pdb=" N THR A 202 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 222 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 230 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 240 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 3.500A pdb=" N CYS A 267 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 274 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 284 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.305A pdb=" N GLY A 305 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 295 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 303 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA8, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.654A pdb=" N ASN A 334 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.707A pdb=" N HIS A 489 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 501 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.814A pdb=" N VAL A 519 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.561A pdb=" N ILE I 41 " --> pdb=" O CYS I 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 51 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU I 70 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS I 124 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 78 through 82 removed outlier: 4.150A pdb=" N GLN I 80 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 98 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 95 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS I 102 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 135 through 137 removed outlier: 7.345A pdb=" N GLN I 155 " --> pdb=" O CYS I 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'I' and resid 160 through 164 removed outlier: 3.840A pdb=" N PHE I 171 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'I' and resid 245 through 252 removed outlier: 4.013A pdb=" N ASP I 247 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 263 " --> pdb=" O ASP I 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 251 " --> pdb=" O SER I 259 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I 262 " --> pdb=" O PHE I 269 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS I 270 " --> pdb=" O ARG I 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 290 through 291 Processing sheet with id=AC3, first strand: chain 'I' and resid 332 through 336 removed outlier: 3.776A pdb=" N ARG I 334 " --> pdb=" O VAL I 346 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY I 336 " --> pdb=" O VAL I 344 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL I 344 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 430 through 432 removed outlier: 3.690A pdb=" N VAL I 440 " --> pdb=" O VAL I 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 472 through 473 removed outlier: 3.628A pdb=" N LEU I 457 " --> pdb=" O PHE I 472 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS I 454 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER I 509 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 546 through 550 removed outlier: 3.520A pdb=" N HIS I 546 " --> pdb=" O SER I 603 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1683 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: 3.00 Time building geometry restraints manager: 1.88 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: 5372 1.34 - 1.46: 2812 1.46 - 1.57: 8938 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 17260 Sorted by residual: bond pdb=" C ASN D 371 " pdb=" N PRO D 372 " ideal model delta sigma weight residual 1.330 1.367 -0.036 1.23e-02 6.61e+03 8.76e+00 bond pdb=" N ASP I 317 " pdb=" CA ASP I 317 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.77e+00 bond pdb=" N PRO A 419 " pdb=" CA PRO A 419 " ideal model delta sigma weight residual 1.473 1.453 0.020 8.50e-03 1.38e+04 5.58e+00 bond pdb=" N GLU A 410 " pdb=" CA GLU A 410 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" C THR I 688 " pdb=" N PRO I 689 " ideal model delta sigma weight residual 1.335 1.357 -0.022 9.40e-03 1.13e+04 5.27e+00 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 23001 3.13 - 6.27: 356 6.27 - 9.40: 58 9.40 - 12.54: 6 12.54 - 15.67: 2 Bond angle restraints: 23423 Sorted by residual: angle pdb=" N PRO A 419 " pdb=" CA PRO A 419 " pdb=" CB PRO A 419 " ideal model delta sigma weight residual 101.88 110.61 -8.73 1.01e+00 9.80e-01 7.48e+01 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" CB PRO A 418 " ideal model delta sigma weight residual 103.08 111.26 -8.18 9.70e-01 1.06e+00 7.11e+01 angle pdb=" N PRO I 369 " pdb=" CA PRO I 369 " pdb=" CB PRO I 369 " ideal model delta sigma weight residual 103.25 111.37 -8.12 1.05e+00 9.07e-01 5.98e+01 angle pdb=" N PRO A 417 " pdb=" CA PRO A 417 " pdb=" CB PRO A 417 " ideal model delta sigma weight residual 103.08 109.96 -6.88 9.70e-01 1.06e+00 5.02e+01 angle pdb=" N PRO I 403 " pdb=" CA PRO I 403 " pdb=" CB PRO I 403 " ideal model delta sigma weight residual 103.51 110.19 -6.68 9.60e-01 1.09e+00 4.84e+01 ... (remaining 23418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9081 17.85 - 35.70: 1065 35.70 - 53.56: 188 53.56 - 71.41: 45 71.41 - 89.26: 23 Dihedral angle restraints: 10402 sinusoidal: 4005 harmonic: 6397 Sorted by residual: dihedral pdb=" CA VAL I 437 " pdb=" C VAL I 437 " pdb=" N PRO I 438 " pdb=" CA PRO I 438 " ideal model delta harmonic sigma weight residual -180.00 -111.84 -68.16 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA ALA I 633 " pdb=" C ALA I 633 " pdb=" N CYS I 634 " pdb=" CA CYS I 634 " ideal model delta harmonic sigma weight residual 180.00 127.53 52.47 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLN H 211 " pdb=" C GLN H 211 " pdb=" N TYR H 212 " pdb=" CA TYR H 212 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 10399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2421 0.089 - 0.178: 233 0.178 - 0.266: 30 0.266 - 0.355: 2 0.355 - 0.444: 2 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE I 534 " pdb=" CA ILE I 534 " pdb=" CG1 ILE I 534 " pdb=" CG2 ILE I 534 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CB VAL I 437 " pdb=" CA VAL I 437 " pdb=" CG1 VAL I 437 " pdb=" CG2 VAL I 437 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA PRO I 369 " pdb=" N PRO I 369 " pdb=" C PRO I 369 " pdb=" CB PRO I 369 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2685 not shown) Planarity restraints: 3011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 409 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL A 409 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 409 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 437 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO I 438 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO I 438 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 438 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 463 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO I 464 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 464 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 464 " -0.049 5.00e-02 4.00e+02 ... (remaining 3008 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4811 2.81 - 3.33: 15432 3.33 - 3.85: 27153 3.85 - 4.38: 30345 4.38 - 4.90: 51167 Nonbonded interactions: 128908 Sorted by model distance: nonbonded pdb=" O SER D 86 " pdb=" OG SER D 86 " model vdw 2.285 3.040 nonbonded pdb=" O VAL I 444 " pdb=" OG1 THR I 484 " model vdw 2.294 3.040 nonbonded pdb=" OG SER I 156 " pdb=" OD1 ASP I 158 " model vdw 2.298 3.040 nonbonded pdb=" O PHE I 86 " pdb=" OH TYR I 127 " model vdw 2.299 3.040 nonbonded pdb=" O GLY I 767 " pdb=" OG1 THR I 771 " model vdw 2.306 3.040 ... (remaining 128903 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17260 Z= 0.254 Angle : 1.005 15.672 23423 Z= 0.564 Chirality : 0.057 0.444 2688 Planarity : 0.007 0.106 3011 Dihedral : 16.304 89.260 6258 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.41 % Favored : 90.31 % Rotamer: Outliers : 0.34 % Allowed : 10.91 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.57 (0.13), residues: 2167 helix: -4.21 (0.09), residues: 813 sheet: -2.87 (0.22), residues: 416 loop : -3.45 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 101 TYR 0.025 0.002 TYR D 361 PHE 0.032 0.002 PHE I 632 TRP 0.025 0.002 TRP A 139 HIS 0.008 0.001 HIS H 192 Details of bonding type rmsd covalent geometry : bond 0.00524 (17260) covalent geometry : angle 1.00491 (23423) hydrogen bonds : bond 0.31534 ( 573) hydrogen bonds : angle 10.31421 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8187 (mmt180) REVERT: A 347 MET cc_start: 0.8346 (mpp) cc_final: 0.8139 (mpp) REVERT: A 578 LEU cc_start: 0.8785 (pp) cc_final: 0.8360 (pp) REVERT: D 246 MET cc_start: 0.8110 (mmt) cc_final: 0.7568 (mmm) REVERT: D 251 ASP cc_start: 0.7759 (m-30) cc_final: 0.7406 (m-30) REVERT: D 260 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8412 (mtt-85) REVERT: D 295 ARG cc_start: 0.8515 (ttt180) cc_final: 0.8304 (ttt90) REVERT: D 343 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: D 361 TYR cc_start: 0.6912 (t80) cc_final: 0.6679 (t80) REVERT: H 53 TYR cc_start: 0.8538 (t80) cc_final: 0.8138 (t80) REVERT: H 186 PHE cc_start: 0.8562 (t80) cc_final: 0.8183 (t80) REVERT: H 190 PHE cc_start: 0.8989 (m-80) cc_final: 0.8654 (m-80) REVERT: H 225 TYR cc_start: 0.8806 (m-10) cc_final: 0.8376 (m-10) REVERT: H 286 CYS cc_start: 0.8593 (t) cc_final: 0.8255 (t) REVERT: H 334 ILE cc_start: 0.9118 (mt) cc_final: 0.8910 (tt) REVERT: H 480 LYS cc_start: 0.9197 (mttt) cc_final: 0.8601 (mmmm) REVERT: I 98 LEU cc_start: 0.8625 (tp) cc_final: 0.8365 (tt) REVERT: I 123 MET cc_start: 0.7284 (mmp) cc_final: 0.7036 (mmp) REVERT: I 138 MET cc_start: 0.7847 (ptm) cc_final: 0.7589 (ptp) REVERT: I 284 ASP cc_start: 0.8432 (p0) cc_final: 0.8188 (p0) REVERT: I 477 MET cc_start: 0.3765 (mmt) cc_final: 0.1971 (mmt) REVERT: I 501 GLU cc_start: 0.8739 (pp20) cc_final: 0.8178 (pp20) REVERT: I 535 CYS cc_start: 0.7271 (t) cc_final: 0.6541 (p) REVERT: I 711 ASP cc_start: 0.9109 (m-30) cc_final: 0.8669 (p0) REVERT: J 69 MET cc_start: 0.8594 (tmm) cc_final: 0.7976 (tmm) REVERT: J 70 HIS cc_start: 0.8170 (t-90) cc_final: 0.7900 (t70) outliers start: 6 outliers final: 3 residues processed: 285 average time/residue: 0.1334 time to fit residues: 56.9304 Evaluate side-chains 204 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 316 HIS A 449 HIS A 504 HIS A 581 HIS D 40 HIS D 103 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS D 366 HIS D 371 ASN D 377 ASN D 384 ASN H 325 ASN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN H 500 GLN I 55 HIS I 120 GLN I 166 GLN I 276 GLN I 307 ASN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 515 ASN I 553 ASN ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 GLN I 719 ASN I 748 GLN I 760 GLN ** I 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.105490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075300 restraints weight = 55301.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077706 restraints weight = 30231.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.079295 restraints weight = 21046.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080363 restraints weight = 16897.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080592 restraints weight = 14736.194| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17260 Z= 0.182 Angle : 0.702 14.459 23423 Z= 0.366 Chirality : 0.044 0.230 2688 Planarity : 0.006 0.098 3011 Dihedral : 6.318 59.253 2338 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.58 % Favored : 91.28 % Rotamer: Outliers : 2.64 % Allowed : 16.30 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.15), residues: 2167 helix: -2.25 (0.14), residues: 860 sheet: -2.20 (0.24), residues: 358 loop : -3.24 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 669 TYR 0.029 0.002 TYR H 304 PHE 0.018 0.002 PHE A 521 TRP 0.010 0.001 TRP I 610 HIS 0.011 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00399 (17260) covalent geometry : angle 0.70183 (23423) hydrogen bonds : bond 0.04804 ( 573) hydrogen bonds : angle 5.93314 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.9538 (m-30) cc_final: 0.9324 (t70) REVERT: A 326 MET cc_start: 0.8197 (mpp) cc_final: 0.7827 (mpp) REVERT: A 570 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: D 246 MET cc_start: 0.8170 (mmt) cc_final: 0.7712 (mmm) REVERT: D 251 ASP cc_start: 0.7475 (m-30) cc_final: 0.7190 (m-30) REVERT: D 260 ARG cc_start: 0.8689 (mtt180) cc_final: 0.8429 (mtt-85) REVERT: D 337 MET cc_start: 0.8895 (tpp) cc_final: 0.7792 (tpp) REVERT: D 339 GLU cc_start: 0.8572 (mp0) cc_final: 0.7971 (mp0) REVERT: D 373 LEU cc_start: 0.7575 (mt) cc_final: 0.7359 (pp) REVERT: H 61 GLN cc_start: 0.6341 (mm-40) cc_final: 0.5268 (mm-40) REVERT: H 186 PHE cc_start: 0.8473 (t80) cc_final: 0.7980 (t80) REVERT: H 190 PHE cc_start: 0.8982 (m-80) cc_final: 0.8430 (m-80) REVERT: H 230 MET cc_start: 0.7562 (mtp) cc_final: 0.6792 (mpp) REVERT: H 295 MET cc_start: 0.9313 (mmt) cc_final: 0.8938 (mpp) REVERT: H 479 GLN cc_start: 0.8819 (tp40) cc_final: 0.8564 (tp40) REVERT: H 480 LYS cc_start: 0.9148 (mttt) cc_final: 0.8660 (mmmm) REVERT: I 123 MET cc_start: 0.7205 (mmp) cc_final: 0.6928 (mmp) REVERT: I 138 MET cc_start: 0.8072 (ptm) cc_final: 0.7661 (ptp) REVERT: I 160 MET cc_start: 0.7326 (ttp) cc_final: 0.7086 (ttt) REVERT: I 239 LEU cc_start: 0.8756 (tp) cc_final: 0.8349 (mt) REVERT: I 477 MET cc_start: 0.4155 (mmt) cc_final: 0.2501 (mmt) REVERT: I 481 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5220 (pt) REVERT: I 535 CYS cc_start: 0.6964 (t) cc_final: 0.6114 (p) REVERT: I 711 ASP cc_start: 0.9079 (m-30) cc_final: 0.8551 (p0) REVERT: I 770 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6441 (tt0) REVERT: J 43 GLU cc_start: 0.9091 (pm20) cc_final: 0.8856 (pm20) REVERT: J 69 MET cc_start: 0.8237 (tmm) cc_final: 0.7643 (tmm) REVERT: J 70 HIS cc_start: 0.7863 (t-90) cc_final: 0.7587 (t70) REVERT: J 71 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8063 (tm-30) outliers start: 47 outliers final: 23 residues processed: 266 average time/residue: 0.1014 time to fit residues: 42.2435 Evaluate side-chains 218 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 425 ASN Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 590 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 144 optimal weight: 0.0770 chunk 105 optimal weight: 0.0270 chunk 176 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS D 309 ASN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 HIS ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077254 restraints weight = 55658.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079880 restraints weight = 29610.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081594 restraints weight = 20178.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082652 restraints weight = 16015.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.083183 restraints weight = 13950.915| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17260 Z= 0.117 Angle : 0.644 11.364 23423 Z= 0.325 Chirality : 0.042 0.221 2688 Planarity : 0.005 0.093 3011 Dihedral : 5.665 57.377 2338 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.89 % Favored : 92.02 % Rotamer: Outliers : 2.81 % Allowed : 18.44 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.16), residues: 2167 helix: -1.32 (0.16), residues: 864 sheet: -1.98 (0.24), residues: 372 loop : -3.06 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 295 TYR 0.019 0.001 TYR H 304 PHE 0.019 0.001 PHE H 238 TRP 0.008 0.001 TRP I 610 HIS 0.014 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00253 (17260) covalent geometry : angle 0.64377 (23423) hydrogen bonds : bond 0.03699 ( 573) hydrogen bonds : angle 5.09565 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9141 (tp) cc_final: 0.8832 (tp) REVERT: A 326 MET cc_start: 0.8219 (mpp) cc_final: 0.7851 (mpp) REVERT: A 581 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.6748 (p-80) REVERT: A 584 MET cc_start: 0.8362 (ppp) cc_final: 0.7522 (ppp) REVERT: D 203 GLU cc_start: 0.8325 (mp0) cc_final: 0.7911 (mp0) REVERT: D 275 ASN cc_start: 0.8263 (m-40) cc_final: 0.8019 (m110) REVERT: D 295 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7949 (ttt90) REVERT: D 337 MET cc_start: 0.8737 (tpp) cc_final: 0.7721 (tpp) REVERT: D 339 GLU cc_start: 0.8504 (mp0) cc_final: 0.8004 (mp0) REVERT: H 43 LEU cc_start: 0.9568 (tp) cc_final: 0.9292 (tt) REVERT: H 186 PHE cc_start: 0.8499 (t80) cc_final: 0.7968 (t80) REVERT: H 190 PHE cc_start: 0.8926 (m-80) cc_final: 0.8418 (m-80) REVERT: H 230 MET cc_start: 0.7293 (mtp) cc_final: 0.6838 (mpp) REVERT: H 295 MET cc_start: 0.9287 (mmt) cc_final: 0.8913 (mpp) REVERT: H 377 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (mm) REVERT: H 391 TYR cc_start: 0.9411 (t80) cc_final: 0.9154 (t80) REVERT: H 405 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9107 (tt) REVERT: H 445 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8295 (mm-40) REVERT: H 480 LYS cc_start: 0.9163 (mttt) cc_final: 0.8685 (mmmm) REVERT: H 482 GLU cc_start: 0.8223 (tt0) cc_final: 0.7745 (mt-10) REVERT: I 82 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: I 123 MET cc_start: 0.7257 (mmp) cc_final: 0.6971 (mmp) REVERT: I 239 LEU cc_start: 0.8723 (tp) cc_final: 0.8433 (mt) REVERT: I 477 MET cc_start: 0.4249 (mmt) cc_final: 0.2686 (mmt) REVERT: I 481 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.5065 (pt) REVERT: I 535 CYS cc_start: 0.6887 (t) cc_final: 0.6510 (t) REVERT: I 580 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7759 (t80) REVERT: I 582 PHE cc_start: 0.5147 (m-80) cc_final: 0.4749 (m-80) REVERT: I 673 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: I 711 ASP cc_start: 0.9031 (m-30) cc_final: 0.8483 (p0) REVERT: J 30 PHE cc_start: 0.8496 (t80) cc_final: 0.8270 (t80) REVERT: J 43 GLU cc_start: 0.8992 (pm20) cc_final: 0.8650 (pm20) REVERT: J 71 GLN cc_start: 0.8288 (tm-30) cc_final: 0.8040 (tm-30) outliers start: 50 outliers final: 23 residues processed: 266 average time/residue: 0.1094 time to fit residues: 46.2753 Evaluate side-chains 234 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 134 optimal weight: 0.0070 chunk 140 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 581 HIS D 155 GLN D 178 HIS D 366 HIS ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.105055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074746 restraints weight = 56119.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077219 restraints weight = 30313.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078821 restraints weight = 21019.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.079784 restraints weight = 16828.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080434 restraints weight = 14780.757| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17260 Z= 0.191 Angle : 0.685 12.343 23423 Z= 0.345 Chirality : 0.044 0.216 2688 Planarity : 0.005 0.089 3011 Dihedral : 5.631 56.747 2338 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.14 % Rotamer: Outliers : 3.71 % Allowed : 19.73 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.17), residues: 2167 helix: -0.88 (0.17), residues: 874 sheet: -1.84 (0.25), residues: 371 loop : -2.99 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 669 TYR 0.033 0.002 TYR D 361 PHE 0.019 0.002 PHE H 238 TRP 0.009 0.001 TRP I 610 HIS 0.016 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00429 (17260) covalent geometry : angle 0.68547 (23423) hydrogen bonds : bond 0.03813 ( 573) hydrogen bonds : angle 5.10806 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8281 (mpp) cc_final: 0.7808 (mpp) REVERT: A 581 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: A 584 MET cc_start: 0.8190 (ppp) cc_final: 0.7841 (ppp) REVERT: D 203 GLU cc_start: 0.8370 (mp0) cc_final: 0.7972 (mp0) REVERT: D 337 MET cc_start: 0.8766 (tpp) cc_final: 0.7872 (tpp) REVERT: D 339 GLU cc_start: 0.8484 (mp0) cc_final: 0.7964 (mp0) REVERT: D 361 TYR cc_start: 0.6697 (t80) cc_final: 0.6318 (t80) REVERT: H 43 LEU cc_start: 0.9584 (tp) cc_final: 0.9228 (tt) REVERT: H 186 PHE cc_start: 0.8540 (t80) cc_final: 0.8005 (t80) REVERT: H 190 PHE cc_start: 0.9044 (m-80) cc_final: 0.8497 (m-80) REVERT: H 295 MET cc_start: 0.9319 (mmt) cc_final: 0.8905 (mpp) REVERT: H 298 MET cc_start: 0.8439 (tmm) cc_final: 0.8092 (tmm) REVERT: H 377 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8362 (mm) REVERT: H 383 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7301 (tp30) REVERT: H 480 LYS cc_start: 0.9212 (mttt) cc_final: 0.8770 (mmmm) REVERT: I 123 MET cc_start: 0.7323 (mmp) cc_final: 0.7092 (mmp) REVERT: I 157 MET cc_start: 0.8338 (mmm) cc_final: 0.8048 (mmm) REVERT: I 239 LEU cc_start: 0.8786 (tp) cc_final: 0.8532 (mt) REVERT: I 477 MET cc_start: 0.4332 (mmt) cc_final: 0.2782 (mmt) REVERT: I 535 CYS cc_start: 0.6812 (t) cc_final: 0.6342 (t) REVERT: I 580 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7906 (t80) REVERT: I 582 PHE cc_start: 0.5003 (m-80) cc_final: 0.4588 (m-80) REVERT: I 622 GLU cc_start: 0.8487 (pt0) cc_final: 0.8074 (tp30) REVERT: I 651 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6609 (p-80) REVERT: I 673 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: I 711 ASP cc_start: 0.9019 (m-30) cc_final: 0.8435 (p0) REVERT: I 770 GLU cc_start: 0.6311 (mt-10) cc_final: 0.6029 (tt0) REVERT: J 43 GLU cc_start: 0.8985 (pm20) cc_final: 0.8585 (pm20) outliers start: 66 outliers final: 38 residues processed: 248 average time/residue: 0.1035 time to fit residues: 41.1086 Evaluate side-chains 236 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 651 HIS Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 123 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 200 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS D 155 GLN D 165 ASN H 61 GLN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.110670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085746 restraints weight = 55444.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085210 restraints weight = 29833.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085733 restraints weight = 25193.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086142 restraints weight = 21491.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086302 restraints weight = 19353.517| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17260 Z= 0.108 Angle : 0.644 12.255 23423 Z= 0.315 Chirality : 0.043 0.218 2688 Planarity : 0.004 0.085 3011 Dihedral : 5.271 54.949 2338 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 2.75 % Allowed : 21.64 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.17), residues: 2167 helix: -0.40 (0.18), residues: 867 sheet: -1.62 (0.25), residues: 351 loop : -2.87 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 669 TYR 0.019 0.001 TYR D 361 PHE 0.019 0.001 PHE H 238 TRP 0.007 0.001 TRP I 741 HIS 0.010 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00243 (17260) covalent geometry : angle 0.64405 (23423) hydrogen bonds : bond 0.03212 ( 573) hydrogen bonds : angle 4.64917 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 MET cc_start: 0.8579 (mmm) cc_final: 0.8082 (tpt) REVERT: A 581 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6817 (p-80) REVERT: D 177 ILE cc_start: 0.9232 (mm) cc_final: 0.9028 (mm) REVERT: D 203 GLU cc_start: 0.8478 (mp0) cc_final: 0.8064 (mp0) REVERT: D 275 ASN cc_start: 0.8063 (m-40) cc_final: 0.7819 (m110) REVERT: D 337 MET cc_start: 0.8551 (tpp) cc_final: 0.7831 (tpp) REVERT: D 339 GLU cc_start: 0.8334 (mp0) cc_final: 0.7931 (mp0) REVERT: H 30 MET cc_start: 0.8891 (mtt) cc_final: 0.8480 (mtm) REVERT: H 43 LEU cc_start: 0.9548 (tp) cc_final: 0.9292 (tt) REVERT: H 50 GLU cc_start: 0.8828 (tp30) cc_final: 0.8615 (tp30) REVERT: H 54 ILE cc_start: 0.8075 (mm) cc_final: 0.7856 (mm) REVERT: H 186 PHE cc_start: 0.8447 (t80) cc_final: 0.7801 (t80) REVERT: H 190 PHE cc_start: 0.8930 (m-80) cc_final: 0.8320 (m-80) REVERT: H 236 LYS cc_start: 0.9341 (tttt) cc_final: 0.9102 (tmtt) REVERT: H 295 MET cc_start: 0.9308 (mmt) cc_final: 0.8870 (mpp) REVERT: H 298 MET cc_start: 0.8574 (tmm) cc_final: 0.8278 (tmm) REVERT: H 377 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8470 (mm) REVERT: H 479 GLN cc_start: 0.8532 (tp40) cc_final: 0.8221 (tt0) REVERT: H 480 LYS cc_start: 0.9112 (mttt) cc_final: 0.8672 (mmmm) REVERT: I 123 MET cc_start: 0.7277 (mmp) cc_final: 0.7043 (mmp) REVERT: I 239 LEU cc_start: 0.8779 (tp) cc_final: 0.8572 (mt) REVERT: I 477 MET cc_start: 0.4232 (mmt) cc_final: 0.2611 (mmt) REVERT: I 481 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.4933 (pt) REVERT: I 535 CYS cc_start: 0.6910 (t) cc_final: 0.6407 (t) REVERT: I 580 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7953 (t80) REVERT: I 582 PHE cc_start: 0.5170 (m-80) cc_final: 0.4738 (m-80) REVERT: I 622 GLU cc_start: 0.8354 (pt0) cc_final: 0.7909 (tp30) REVERT: I 635 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6849 (p) REVERT: I 673 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: I 711 ASP cc_start: 0.8883 (m-30) cc_final: 0.8275 (p0) REVERT: I 770 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5874 (tt0) outliers start: 49 outliers final: 27 residues processed: 257 average time/residue: 0.1075 time to fit residues: 44.5968 Evaluate side-chains 231 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.102941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072525 restraints weight = 56328.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074908 restraints weight = 30970.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076426 restraints weight = 21745.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077327 restraints weight = 17586.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077987 restraints weight = 15461.442| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17260 Z= 0.296 Angle : 0.769 11.812 23423 Z= 0.389 Chirality : 0.048 0.478 2688 Planarity : 0.005 0.087 3011 Dihedral : 5.718 55.095 2337 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.38 % Favored : 89.52 % Rotamer: Outliers : 3.99 % Allowed : 21.59 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.17), residues: 2167 helix: -0.58 (0.17), residues: 877 sheet: -1.93 (0.24), residues: 389 loop : -2.97 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 101 TYR 0.027 0.002 TYR H 304 PHE 0.025 0.002 PHE H 238 TRP 0.012 0.002 TRP I 9 HIS 0.013 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00656 (17260) covalent geometry : angle 0.76854 (23423) hydrogen bonds : bond 0.04134 ( 573) hydrogen bonds : angle 5.25566 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7218 (mmm-85) REVERT: A 581 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.6796 (p-80) REVERT: D 203 GLU cc_start: 0.8429 (mp0) cc_final: 0.7953 (mp0) REVERT: D 337 MET cc_start: 0.8814 (tpp) cc_final: 0.7992 (tpp) REVERT: D 339 GLU cc_start: 0.8511 (mp0) cc_final: 0.7955 (mp0) REVERT: H 50 GLU cc_start: 0.8812 (tp30) cc_final: 0.8425 (mm-30) REVERT: H 186 PHE cc_start: 0.8626 (t80) cc_final: 0.8410 (t80) REVERT: H 190 PHE cc_start: 0.9129 (m-80) cc_final: 0.8831 (m-80) REVERT: H 295 MET cc_start: 0.9320 (mmt) cc_final: 0.8839 (mpp) REVERT: H 377 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8507 (mm) REVERT: H 412 LEU cc_start: 0.9371 (mm) cc_final: 0.8859 (mm) REVERT: H 479 GLN cc_start: 0.8781 (tp40) cc_final: 0.8508 (tp40) REVERT: H 480 LYS cc_start: 0.9246 (mttt) cc_final: 0.8777 (mmmm) REVERT: I 123 MET cc_start: 0.7298 (mmp) cc_final: 0.7080 (mmp) REVERT: I 239 LEU cc_start: 0.8790 (tp) cc_final: 0.8555 (mt) REVERT: I 477 MET cc_start: 0.4249 (mmt) cc_final: 0.2493 (mmt) REVERT: I 481 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5379 (pt) REVERT: I 622 GLU cc_start: 0.8506 (pt0) cc_final: 0.8184 (tp30) REVERT: I 673 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: I 770 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6092 (tt0) REVERT: J 43 GLU cc_start: 0.9036 (pm20) cc_final: 0.8818 (pm20) outliers start: 71 outliers final: 48 residues processed: 239 average time/residue: 0.1176 time to fit residues: 44.9309 Evaluate side-chains 228 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 289 CYS Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 525 CYS Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 640 ILE Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Chi-restraints excluded: chain I residue 766 LEU Chi-restraints excluded: chain J residue 45 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 156 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 181 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076103 restraints weight = 55322.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078563 restraints weight = 30075.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080111 restraints weight = 20763.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081181 restraints weight = 16675.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.081843 restraints weight = 14554.787| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17260 Z= 0.123 Angle : 0.681 12.268 23423 Z= 0.333 Chirality : 0.044 0.210 2688 Planarity : 0.004 0.081 3011 Dihedral : 5.332 54.824 2337 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.08 % Favored : 91.83 % Rotamer: Outliers : 2.70 % Allowed : 23.66 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.18), residues: 2167 helix: -0.13 (0.18), residues: 879 sheet: -1.70 (0.25), residues: 372 loop : -2.91 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 528 TYR 0.018 0.001 TYR H 304 PHE 0.020 0.001 PHE H 238 TRP 0.007 0.001 TRP I 741 HIS 0.012 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00282 (17260) covalent geometry : angle 0.68059 (23423) hydrogen bonds : bond 0.03272 ( 573) hydrogen bonds : angle 4.65231 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 MET cc_start: 0.8735 (mmm) cc_final: 0.8529 (mmm) REVERT: A 581 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.6817 (p-80) REVERT: D 203 GLU cc_start: 0.8446 (mp0) cc_final: 0.7991 (mp0) REVERT: D 275 ASN cc_start: 0.8311 (m-40) cc_final: 0.8014 (m110) REVERT: D 337 MET cc_start: 0.8649 (tpp) cc_final: 0.7941 (tpp) REVERT: D 339 GLU cc_start: 0.8428 (mp0) cc_final: 0.7917 (mp0) REVERT: H 26 LEU cc_start: 0.9331 (tt) cc_final: 0.9119 (mt) REVERT: H 43 LEU cc_start: 0.9571 (tp) cc_final: 0.9199 (tt) REVERT: H 50 GLU cc_start: 0.8770 (tp30) cc_final: 0.8490 (tp30) REVERT: H 54 ILE cc_start: 0.8154 (mm) cc_final: 0.7907 (mm) REVERT: H 186 PHE cc_start: 0.8522 (t80) cc_final: 0.8289 (t80) REVERT: H 190 PHE cc_start: 0.9012 (m-80) cc_final: 0.8691 (m-80) REVERT: H 295 MET cc_start: 0.9263 (mmt) cc_final: 0.8867 (mpp) REVERT: H 377 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8427 (mm) REVERT: H 412 LEU cc_start: 0.9234 (mm) cc_final: 0.8974 (mm) REVERT: H 479 GLN cc_start: 0.8616 (tp40) cc_final: 0.8248 (tt0) REVERT: H 480 LYS cc_start: 0.9161 (mttt) cc_final: 0.8690 (mmmm) REVERT: H 482 GLU cc_start: 0.8286 (tt0) cc_final: 0.7846 (mt-10) REVERT: I 123 MET cc_start: 0.7210 (mmp) cc_final: 0.6966 (mmp) REVERT: I 239 LEU cc_start: 0.8790 (tp) cc_final: 0.8572 (mt) REVERT: I 477 MET cc_start: 0.4314 (mmt) cc_final: 0.2804 (mmt) REVERT: I 481 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5021 (pt) REVERT: I 580 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7929 (t80) REVERT: I 622 GLU cc_start: 0.8382 (pt0) cc_final: 0.8058 (tp30) REVERT: I 635 SER cc_start: 0.7214 (OUTLIER) cc_final: 0.6882 (p) REVERT: I 673 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: I 770 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5950 (tt0) REVERT: J 43 GLU cc_start: 0.9002 (pm20) cc_final: 0.8750 (pm20) outliers start: 48 outliers final: 32 residues processed: 235 average time/residue: 0.0971 time to fit residues: 36.9061 Evaluate side-chains 225 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 580 PHE Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 150 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.106230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075907 restraints weight = 55721.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078412 restraints weight = 29971.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080079 restraints weight = 20752.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081154 restraints weight = 16556.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081691 restraints weight = 14437.518| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17260 Z= 0.132 Angle : 0.677 12.513 23423 Z= 0.331 Chirality : 0.044 0.236 2688 Planarity : 0.004 0.081 3011 Dihedral : 5.227 53.355 2337 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.09 % Favored : 90.82 % Rotamer: Outliers : 2.75 % Allowed : 23.61 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.18), residues: 2167 helix: 0.04 (0.18), residues: 874 sheet: -1.60 (0.25), residues: 375 loop : -2.82 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 528 TYR 0.022 0.001 TYR H 304 PHE 0.028 0.001 PHE H 271 TRP 0.006 0.001 TRP I 237 HIS 0.009 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00304 (17260) covalent geometry : angle 0.67733 (23423) hydrogen bonds : bond 0.03344 ( 573) hydrogen bonds : angle 4.60490 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 448 MET cc_start: 0.8724 (mmm) cc_final: 0.8443 (tpp) REVERT: A 581 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7198 (p90) REVERT: D 203 GLU cc_start: 0.8440 (mp0) cc_final: 0.7992 (mp0) REVERT: D 275 ASN cc_start: 0.8259 (m-40) cc_final: 0.7946 (m110) REVERT: D 337 MET cc_start: 0.8631 (tpp) cc_final: 0.7931 (tpp) REVERT: D 339 GLU cc_start: 0.8393 (mp0) cc_final: 0.7765 (mp0) REVERT: H 26 LEU cc_start: 0.9341 (tt) cc_final: 0.9136 (mt) REVERT: H 43 LEU cc_start: 0.9585 (tp) cc_final: 0.9221 (tt) REVERT: H 50 GLU cc_start: 0.8767 (tp30) cc_final: 0.8494 (tp30) REVERT: H 54 ILE cc_start: 0.8212 (mm) cc_final: 0.7929 (mm) REVERT: H 186 PHE cc_start: 0.8496 (t80) cc_final: 0.8260 (t80) REVERT: H 190 PHE cc_start: 0.9011 (m-80) cc_final: 0.8669 (m-80) REVERT: H 295 MET cc_start: 0.9322 (mmt) cc_final: 0.8915 (mpp) REVERT: H 377 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8424 (mm) REVERT: H 412 LEU cc_start: 0.9221 (mm) cc_final: 0.9012 (mm) REVERT: H 479 GLN cc_start: 0.8631 (tp40) cc_final: 0.8247 (tt0) REVERT: H 480 LYS cc_start: 0.9179 (mttt) cc_final: 0.8704 (mmmm) REVERT: I 123 MET cc_start: 0.7179 (mmp) cc_final: 0.6931 (mmp) REVERT: I 239 LEU cc_start: 0.8837 (tp) cc_final: 0.8616 (mt) REVERT: I 477 MET cc_start: 0.4402 (mmt) cc_final: 0.2862 (mmt) REVERT: I 481 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5090 (pt) REVERT: I 622 GLU cc_start: 0.8417 (pt0) cc_final: 0.8089 (tp30) REVERT: I 635 SER cc_start: 0.7205 (OUTLIER) cc_final: 0.6864 (p) REVERT: I 673 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: I 770 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5937 (tt0) REVERT: J 43 GLU cc_start: 0.8991 (pm20) cc_final: 0.8639 (pm20) outliers start: 49 outliers final: 38 residues processed: 234 average time/residue: 0.1091 time to fit residues: 41.2451 Evaluate side-chains 234 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 495 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 315 TYR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 546 HIS Chi-restraints excluded: chain I residue 590 VAL Chi-restraints excluded: chain I residue 599 TYR Chi-restraints excluded: chain I residue 620 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain I residue 673 PHE Chi-restraints excluded: chain I residue 696 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2105 > 50: distance: 19 - 40: 30.016 distance: 35 - 40: 26.602 distance: 40 - 41: 30.156 distance: 41 - 42: 24.824 distance: 41 - 44: 43.262 distance: 42 - 43: 33.196 distance: 42 - 51: 20.414 distance: 44 - 45: 44.948 distance: 45 - 46: 51.703 distance: 46 - 47: 30.584 distance: 47 - 48: 23.691 distance: 48 - 49: 26.589 distance: 48 - 50: 9.356 distance: 52 - 53: 21.460 distance: 52 - 55: 23.072 distance: 53 - 54: 19.343 distance: 53 - 60: 39.865 distance: 55 - 56: 29.946 distance: 56 - 57: 31.405 distance: 57 - 58: 5.900 distance: 57 - 59: 49.699 distance: 60 - 61: 38.181 distance: 61 - 64: 8.728 distance: 62 - 63: 7.743 distance: 62 - 67: 29.741 distance: 64 - 65: 31.746 distance: 64 - 66: 3.595 distance: 67 - 68: 9.786 distance: 72 - 73: 38.461 distance: 73 - 74: 40.790 distance: 73 - 76: 3.029 distance: 74 - 75: 39.956 distance: 76 - 77: 34.219 distance: 77 - 78: 13.391 distance: 78 - 80: 22.685 distance: 82 - 83: 30.513 distance: 82 - 85: 69.550 distance: 83 - 84: 31.421 distance: 83 - 90: 18.615 distance: 85 - 86: 39.926 distance: 86 - 87: 53.724 distance: 87 - 88: 16.965 distance: 87 - 89: 32.365 distance: 90 - 91: 25.669 distance: 90 - 96: 14.374 distance: 91 - 92: 12.338 distance: 91 - 94: 10.322 distance: 92 - 93: 32.011 distance: 92 - 97: 28.013 distance: 94 - 95: 42.432 distance: 95 - 96: 41.334 distance: 97 - 98: 17.508 distance: 98 - 99: 14.081 distance: 98 - 101: 30.286 distance: 99 - 100: 36.381 distance: 99 - 105: 28.902 distance: 101 - 102: 25.859 distance: 102 - 103: 28.676 distance: 102 - 104: 20.269 distance: 105 - 106: 21.928 distance: 106 - 107: 34.372 distance: 106 - 109: 42.978 distance: 107 - 108: 39.256 distance: 107 - 111: 15.372 distance: 111 - 112: 29.066 distance: 112 - 113: 6.418 distance: 112 - 115: 40.789 distance: 113 - 119: 34.643 distance: 115 - 116: 39.987 distance: 115 - 117: 57.554 distance: 116 - 118: 35.792