Starting phenix.real_space_refine on Wed Aug 5 10:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.map" model { file = "/net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xuo_67273/08_2026/9xuo_67273.cif" } resolution = 3.41 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 29 5.16 5 C 5803 2.51 5 N 1588 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4414 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 554} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4584 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 27, 'TRANS': 559} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.20 Number of scatterers: 9041 At special positions: 0 Unit cell: (73.95, 96.9, 144.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 29 16.00 O 1620 8.00 N 1588 7.00 C 5803 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 243.0 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 58.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.786A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.229A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 50 removed outlier: 3.579A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.593A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 4.387A pdb=" N HIS C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.788A pdb=" N VAL C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.570A pdb=" N ARG C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'C' and resid 139 through 156 removed outlier: 4.632A pdb=" N PHE C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.888A pdb=" N ARG C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.800A pdb=" N GLN C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.970A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 236 removed outlier: 3.704A pdb=" N THR C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 266 removed outlier: 4.001A pdb=" N SER C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N MET C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.666A pdb=" N CYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.639A pdb=" N THR C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 299' Processing helix chain 'C' and resid 302 through 316 removed outlier: 4.363A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 387 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 442 through 452 removed outlier: 3.919A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.975A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 521 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.587A pdb=" N GLN C 568 " --> pdb=" O ARG C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 17 Processing helix chain 'D' and resid 20 through 43 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.718A pdb=" N MET D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 removed outlier: 3.514A pdb=" N ALA D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 62 through 73 removed outlier: 4.126A pdb=" N PHE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 102 removed outlier: 4.104A pdb=" N ARG D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.509A pdb=" N LYS D 117 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.964A pdb=" N TRP D 122 " --> pdb=" O PRO D 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.873A pdb=" N LEU D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Proline residue: D 142 - end of helix Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.695A pdb=" N LEU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 removed outlier: 4.218A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 5.190A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 211 removed outlier: 4.343A pdb=" N ASN D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 217 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.600A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 274 removed outlier: 4.081A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.965A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 removed outlier: 3.782A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 311 through 329 removed outlier: 4.020A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 320 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 391 through 398 Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.667A pdb=" N GLN D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 490 through 500 removed outlier: 3.939A pdb=" N ALA D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 532 removed outlier: 3.956A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 547 removed outlier: 3.501A pdb=" N LEU D 547 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 575 through 585 Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AA2, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AA4, first strand: chain 'D' and resid 366 through 369 removed outlier: 3.893A pdb=" N ALA D 366 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 357 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU D 355 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 366 through 369 removed outlier: 3.893A pdb=" N ALA D 366 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 357 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU D 355 " --> pdb=" O PRO D 368 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ALA D 352 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG D 407 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 354 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 405 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 382 through 383 removed outlier: 6.572A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN D 557 " --> pdb=" O ARG D 560 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1023 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: 1.31 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 3667 1.39 - 1.56: 5499 1.56 - 1.72: 0 1.72 - 1.89: 55 1.89 - 2.06: 4 Bond restraints: 9225 Sorted by residual: bond pdb=" C ALA D 173 " pdb=" N PRO D 174 " ideal model delta sigma weight residual 1.332 1.352 -0.020 8.90e-03 1.26e+04 4.89e+00 bond pdb=" C LEU C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.82e+00 bond pdb=" CA THR D 345 " pdb=" CB THR D 345 " ideal model delta sigma weight residual 1.524 1.537 -0.014 1.33e-02 5.65e+03 1.04e+00 bond pdb=" CB VAL C 423 " pdb=" CG2 VAL C 423 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" C ILE D 176 " pdb=" N PRO D 177 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.57e-01 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12059 1.62 - 3.24: 393 3.24 - 4.86: 65 4.86 - 6.47: 21 6.47 - 8.09: 8 Bond angle restraints: 12546 Sorted by residual: angle pdb=" N ILE D 225 " pdb=" CA ILE D 225 " pdb=" C ILE D 225 " ideal model delta sigma weight residual 112.96 106.11 6.85 1.00e+00 1.00e+00 4.70e+01 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 113.20 108.72 4.48 9.60e-01 1.09e+00 2.17e+01 angle pdb=" N LEU D 178 " pdb=" CA LEU D 178 " pdb=" C LEU D 178 " ideal model delta sigma weight residual 113.18 107.40 5.78 1.33e+00 5.65e-01 1.89e+01 angle pdb=" N GLU C 510 " pdb=" CA GLU C 510 " pdb=" C GLU C 510 " ideal model delta sigma weight residual 113.88 109.09 4.79 1.23e+00 6.61e-01 1.51e+01 angle pdb=" C ARG D 534 " pdb=" N GLN D 535 " pdb=" CA GLN D 535 " ideal model delta sigma weight residual 121.54 115.15 6.39 1.91e+00 2.74e-01 1.12e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4825 17.75 - 35.50: 529 35.50 - 53.24: 116 53.24 - 70.99: 11 70.99 - 88.74: 5 Dihedral angle restraints: 5486 sinusoidal: 2158 harmonic: 3328 Sorted by residual: dihedral pdb=" CA ILE C 449 " pdb=" C ILE C 449 " pdb=" N LEU C 450 " pdb=" CA LEU C 450 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR C 329 " pdb=" C THR C 329 " pdb=" N GLN C 330 " pdb=" CA GLN C 330 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 441 " pdb=" C ASP D 441 " pdb=" N ASN D 442 " pdb=" CA ASN D 442 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 828 0.032 - 0.064: 437 0.064 - 0.096: 132 0.096 - 0.128: 49 0.128 - 0.160: 6 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CG LEU C 450 " pdb=" CB LEU C 450 " pdb=" CD1 LEU C 450 " pdb=" CD2 LEU C 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB ILE C 543 " pdb=" CA ILE C 543 " pdb=" CG1 ILE C 543 " pdb=" CG2 ILE C 543 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASP C 401 " pdb=" N ASP C 401 " pdb=" C ASP C 401 " pdb=" CB ASP C 401 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1449 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 5 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ARG D 5 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG D 5 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN D 6 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 61 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 62 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 134 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C TYR C 134 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR C 134 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 135 " -0.011 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 160 2.67 - 3.23: 9031 3.23 - 3.78: 13069 3.78 - 4.34: 17531 4.34 - 4.90: 28472 Nonbonded interactions: 68263 Sorted by model distance: nonbonded pdb=" OD1 ASP D 517 " pdb=" OG SER D 520 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR D 402 " pdb=" OE2 GLU D 412 " model vdw 2.128 3.040 nonbonded pdb=" O THR C 347 " pdb=" OG1 THR C 381 " model vdw 2.201 3.040 nonbonded pdb=" O HIS D 519 " pdb=" NH1 ARG D 523 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP D 460 " pdb=" OG SER D 465 " model vdw 2.246 3.040 ... (remaining 68258 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.000 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.343 9226 Z= 0.198 Angle : 0.746 8.093 12546 Z= 0.414 Chirality : 0.043 0.160 1452 Planarity : 0.004 0.051 1602 Dihedral : 15.303 88.738 3340 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.21), residues: 1156 helix: -2.57 (0.17), residues: 627 sheet: -4.56 (0.60), residues: 40 loop : -3.66 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 96 TYR 0.027 0.002 TYR C 348 PHE 0.014 0.001 PHE C 301 TRP 0.013 0.001 TRP D 163 HIS 0.005 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 9225) covalent geometry : angle 0.74603 / 0.41 (12546) hydrogen bonds : bond 0.12694 / 9.45 ( 357) hydrogen bonds : angle 5.99654 / 3.99 ( 1023) Misc. bond : bond 0.34293 / 18.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 251 MET cc_start: 0.7756 (tpp) cc_final: 0.7543 (tpt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0949 time to fit residues: 13.3845 Evaluate side-chains 75 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 248 GLN C 394 GLN C 424 HIS C 491 HIS D 115 GLN D 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083395 restraints weight = 21884.321| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.41 r_work: 0.3062 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 9226 Z= 0.147 Angle : 0.659 11.000 12546 Z= 0.325 Chirality : 0.041 0.154 1452 Planarity : 0.004 0.051 1602 Dihedral : 6.266 79.745 1272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 1.39 % Allowed : 15.28 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.23), residues: 1156 helix: -1.61 (0.20), residues: 627 sheet: -4.16 (0.62), residues: 40 loop : -3.22 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 22 TYR 0.020 0.001 TYR C 348 PHE 0.011 0.001 PHE C 291 TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9225) covalent geometry : angle 0.65916 / 0.33 (12546) hydrogen bonds : bond 0.04669 / 3.10 ( 357) hydrogen bonds : angle 4.89739 / 3.34 ( 1023) Misc. bond : bond 0.09926 / 5.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 126 ASP cc_start: 0.8665 (m-30) cc_final: 0.8382 (t0) REVERT: C 251 MET cc_start: 0.8025 (tpp) cc_final: 0.7652 (tpt) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.0751 time to fit residues: 10.5869 Evaluate side-chains 86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 chunk 84 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084140 restraints weight = 21710.170| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.41 r_work: 0.3071 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 9226 Z= 0.134 Angle : 0.633 10.890 12546 Z= 0.310 Chirality : 0.041 0.153 1452 Planarity : 0.004 0.052 1602 Dihedral : 6.023 79.292 1272 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.24 % Allowed : 16.35 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.24), residues: 1156 helix: -1.19 (0.21), residues: 628 sheet: -3.42 (0.91), residues: 24 loop : -2.96 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 22 TYR 0.016 0.001 TYR C 348 PHE 0.011 0.001 PHE C 291 TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9225) covalent geometry : angle 0.63332 / 0.31 (12546) hydrogen bonds : bond 0.04308 / 2.86 ( 357) hydrogen bonds : angle 4.67563 / 3.20 ( 1023) Misc. bond : bond 0.13154 / 6.92 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.7023 (mmm) cc_final: 0.6729 (mmm) REVERT: C 126 ASP cc_start: 0.8647 (m-30) cc_final: 0.8331 (t0) REVERT: C 251 MET cc_start: 0.8016 (tpp) cc_final: 0.7642 (tpt) REVERT: C 500 GLU cc_start: 0.7684 (pm20) cc_final: 0.7142 (pm20) REVERT: D 224 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8052 (tp30) REVERT: D 339 GLU cc_start: 0.8604 (tp30) cc_final: 0.8092 (tp30) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.0838 time to fit residues: 12.0284 Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 GLN C 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086967 restraints weight = 22125.175| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.48 r_work: 0.3132 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 9226 Z= 0.107 Angle : 0.592 7.918 12546 Z= 0.290 Chirality : 0.040 0.215 1452 Planarity : 0.003 0.052 1602 Dihedral : 5.720 78.357 1272 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.14 % Allowed : 18.48 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.25), residues: 1156 helix: -0.76 (0.22), residues: 631 sheet: -2.97 (0.90), residues: 24 loop : -2.79 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 422 TYR 0.014 0.001 TYR C 348 PHE 0.008 0.001 PHE C 291 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.000 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9225) covalent geometry : angle 0.59189 / 0.29 (12546) hydrogen bonds : bond 0.03389 / 2.21 ( 357) hydrogen bonds : angle 4.29778 / 2.93 ( 1023) Misc. bond : bond 0.10949 / 5.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 17 MET cc_start: 0.8352 (ppp) cc_final: 0.7878 (ppp) REVERT: C 36 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 84 SER cc_start: 0.9184 (t) cc_final: 0.8908 (p) REVERT: C 251 MET cc_start: 0.7964 (tpp) cc_final: 0.7636 (tpt) REVERT: C 500 GLU cc_start: 0.7709 (pm20) cc_final: 0.7475 (pm20) REVERT: C 527 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9158 (tt) REVERT: C 559 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5588 (mt) REVERT: D 212 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: D 224 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7930 (tp30) REVERT: D 553 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8906 (mt) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.0713 time to fit residues: 10.6531 Evaluate side-chains 92 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 553 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 HIS D 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082598 restraints weight = 22358.251| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.43 r_work: 0.3040 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 9226 Z= 0.198 Angle : 0.674 11.142 12546 Z= 0.327 Chirality : 0.043 0.193 1452 Planarity : 0.004 0.057 1602 Dihedral : 5.863 80.260 1272 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.74 % Allowed : 19.44 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.24), residues: 1156 helix: -0.82 (0.21), residues: 632 sheet: -3.51 (0.65), residues: 41 loop : -2.75 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.014 0.001 TYR C 348 PHE 0.014 0.001 PHE D 32 TRP 0.012 0.001 TRP D 554 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 9225) covalent geometry : angle 0.67419 / 0.33 (12546) hydrogen bonds : bond 0.04955 / 3.31 ( 357) hydrogen bonds : angle 4.62485 / 3.17 ( 1023) Misc. bond : bond 0.15500 / 8.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: C 17 MET cc_start: 0.8525 (ppp) cc_final: 0.8114 (ppp) REVERT: C 36 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8732 (tt) REVERT: C 126 ASP cc_start: 0.8645 (m-30) cc_final: 0.8313 (t0) REVERT: C 251 MET cc_start: 0.8114 (tpp) cc_final: 0.7686 (tpt) REVERT: C 385 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: D 212 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8579 (mtp) outliers start: 35 outliers final: 19 residues processed: 107 average time/residue: 0.0724 time to fit residues: 11.4713 Evaluate side-chains 94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085187 restraints weight = 21984.336| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.40 r_work: 0.3104 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 9226 Z= 0.113 Angle : 0.618 8.381 12546 Z= 0.299 Chirality : 0.040 0.213 1452 Planarity : 0.003 0.055 1602 Dihedral : 5.692 78.462 1272 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.88 % Allowed : 20.73 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.25), residues: 1156 helix: -0.49 (0.21), residues: 638 sheet: -2.88 (0.90), residues: 24 loop : -2.60 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 374 TYR 0.013 0.001 TYR C 348 PHE 0.008 0.001 PHE C 160 TRP 0.011 0.001 TRP D 554 HIS 0.002 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9225) covalent geometry : angle 0.61803 / 0.30 (12546) hydrogen bonds : bond 0.03748 / 2.48 ( 357) hydrogen bonds : angle 4.36875 / 2.98 ( 1023) Misc. bond : bond 0.14243 / 7.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 17 MET cc_start: 0.8357 (ppp) cc_final: 0.8017 (ppp) REVERT: C 36 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8691 (tt) REVERT: C 186 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8761 (tppt) REVERT: C 251 MET cc_start: 0.8053 (tpp) cc_final: 0.7689 (tpt) REVERT: C 385 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: D 212 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: D 224 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7857 (tp30) outliers start: 27 outliers final: 19 residues processed: 98 average time/residue: 0.0717 time to fit residues: 10.7989 Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082956 restraints weight = 22403.447| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.39 r_work: 0.3055 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 9226 Z= 0.183 Angle : 0.680 10.054 12546 Z= 0.324 Chirality : 0.043 0.206 1452 Planarity : 0.004 0.057 1602 Dihedral : 5.765 79.871 1272 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.42 % Allowed : 21.05 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.25), residues: 1156 helix: -0.51 (0.21), residues: 633 sheet: -2.84 (0.94), residues: 24 loop : -2.57 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 422 TYR 0.014 0.001 TYR C 348 PHE 0.012 0.001 PHE D 32 TRP 0.014 0.001 TRP D 554 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 9225) covalent geometry : angle 0.68030 / 0.32 (12546) hydrogen bonds : bond 0.04605 / 3.07 ( 357) hydrogen bonds : angle 4.52680 / 3.09 ( 1023) Misc. bond : bond 0.16474 / 8.67 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.346 Fit side-chains REVERT: C 17 MET cc_start: 0.8497 (ppp) cc_final: 0.8151 (ppp) REVERT: C 36 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8721 (tt) REVERT: C 186 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8732 (tppt) REVERT: C 248 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: C 251 MET cc_start: 0.8128 (tpp) cc_final: 0.7716 (tpt) REVERT: C 396 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: D 212 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8556 (mtp) outliers start: 32 outliers final: 20 residues processed: 101 average time/residue: 0.0761 time to fit residues: 11.6054 Evaluate side-chains 94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086202 restraints weight = 21848.993| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.39 r_work: 0.3124 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 9226 Z= 0.110 Angle : 0.636 11.444 12546 Z= 0.304 Chirality : 0.041 0.196 1452 Planarity : 0.003 0.056 1602 Dihedral : 5.586 77.932 1272 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.56 % Allowed : 22.54 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.25), residues: 1156 helix: -0.18 (0.22), residues: 630 sheet: -2.74 (0.92), residues: 24 loop : -2.45 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 522 TYR 0.013 0.001 TYR C 348 PHE 0.007 0.001 PHE C 160 TRP 0.011 0.001 TRP D 163 HIS 0.002 0.000 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9225) covalent geometry : angle 0.63570 / 0.30 (12546) hydrogen bonds : bond 0.03584 / 2.35 ( 357) hydrogen bonds : angle 4.30217 / 2.93 ( 1023) Misc. bond : bond 0.14352 / 7.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.321 Fit side-chains REVERT: C 17 MET cc_start: 0.8374 (ppp) cc_final: 0.8114 (ppp) REVERT: C 36 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 60 MET cc_start: 0.6579 (mmm) cc_final: 0.6166 (mmm) REVERT: C 186 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8746 (tppt) REVERT: C 251 MET cc_start: 0.8064 (tpp) cc_final: 0.7718 (tpt) REVERT: C 384 GLN cc_start: 0.8416 (mp10) cc_final: 0.8155 (mt0) REVERT: C 385 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: C 396 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8077 (pp20) REVERT: D 73 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7471 (t80) REVERT: D 212 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8476 (mtp) REVERT: D 224 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7766 (tp30) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 0.0729 time to fit residues: 10.6102 Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086594 restraints weight = 21781.351| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.38 r_work: 0.3130 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 9226 Z= 0.112 Angle : 0.642 14.324 12546 Z= 0.303 Chirality : 0.040 0.187 1452 Planarity : 0.003 0.057 1602 Dihedral : 5.485 78.295 1272 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.78 % Allowed : 22.65 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.25), residues: 1156 helix: -0.01 (0.22), residues: 632 sheet: -2.32 (0.98), residues: 24 loop : -2.39 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 538 TYR 0.012 0.001 TYR C 348 PHE 0.007 0.001 PHE C 164 TRP 0.020 0.001 TRP D 550 HIS 0.002 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9225) covalent geometry : angle 0.64194 / 0.30 (12546) hydrogen bonds : bond 0.03542 / 2.34 ( 357) hydrogen bonds : angle 4.21765 / 2.88 ( 1023) Misc. bond : bond 0.14921 / 7.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.344 Fit side-chains REVERT: C 17 MET cc_start: 0.8348 (ppp) cc_final: 0.8088 (ppp) REVERT: C 36 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 60 MET cc_start: 0.6599 (mmm) cc_final: 0.6210 (mmm) REVERT: C 186 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8753 (tppt) REVERT: C 251 MET cc_start: 0.8066 (tpp) cc_final: 0.7717 (tpt) REVERT: C 384 GLN cc_start: 0.8442 (mp10) cc_final: 0.8179 (mt0) REVERT: C 385 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: C 396 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: D 73 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7534 (t80) REVERT: D 212 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8401 (mtp) REVERT: D 224 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7849 (tp30) outliers start: 26 outliers final: 19 residues processed: 100 average time/residue: 0.0611 time to fit residues: 9.4476 Evaluate side-chains 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.0040 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087136 restraints weight = 21763.640| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.31 r_work: 0.3145 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 9226 Z= 0.109 Angle : 0.629 12.378 12546 Z= 0.297 Chirality : 0.040 0.187 1452 Planarity : 0.003 0.055 1602 Dihedral : 5.430 78.239 1272 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.78 % Allowed : 22.86 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.26), residues: 1156 helix: 0.12 (0.22), residues: 631 sheet: -2.26 (0.98), residues: 24 loop : -2.30 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 538 TYR 0.012 0.001 TYR C 348 PHE 0.007 0.001 PHE C 160 TRP 0.019 0.001 TRP D 550 HIS 0.002 0.000 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9225) covalent geometry : angle 0.62879 / 0.30 (12546) hydrogen bonds : bond 0.03488 / 2.32 ( 357) hydrogen bonds : angle 4.17064 / 2.84 ( 1023) Misc. bond : bond 0.14719 / 7.75 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.336 Fit side-chains REVERT: C 17 MET cc_start: 0.8329 (ppp) cc_final: 0.8089 (ppp) REVERT: C 36 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8619 (tt) REVERT: C 60 MET cc_start: 0.6590 (mmm) cc_final: 0.6201 (mmm) REVERT: C 186 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8728 (tppt) REVERT: C 251 MET cc_start: 0.8055 (tpp) cc_final: 0.7709 (tpt) REVERT: C 384 GLN cc_start: 0.8482 (mp10) cc_final: 0.8240 (mt0) REVERT: C 385 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: C 396 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: D 73 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7624 (t80) REVERT: D 185 MET cc_start: 0.4507 (ptt) cc_final: 0.4025 (tpt) REVERT: D 224 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7441 (tp30) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.0645 time to fit residues: 9.7775 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 101 GLN D 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086626 restraints weight = 21543.764| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.34 r_work: 0.3132 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 9226 Z= 0.115 Angle : 0.629 12.182 12546 Z= 0.298 Chirality : 0.040 0.182 1452 Planarity : 0.003 0.055 1602 Dihedral : 5.432 78.353 1272 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.10 % Allowed : 22.65 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 1156 helix: 0.19 (0.22), residues: 624 sheet: -2.10 (1.05), residues: 24 loop : -2.28 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.012 0.001 TYR C 348 PHE 0.008 0.001 PHE C 160 TRP 0.020 0.001 TRP D 550 HIS 0.002 0.000 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 9225) covalent geometry : angle 0.62917 / 0.30 (12546) hydrogen bonds : bond 0.03548 / 2.36 ( 357) hydrogen bonds : angle 4.17895 / 2.85 ( 1023) Misc. bond : bond 0.14702 / 7.74 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.30 seconds wall clock time: 30 minutes 51.46 seconds (1851.46 seconds total)