Starting phenix.real_space_refine on Thu Jul 2 15:16:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.cif" model { file = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7a_36936/07_2026/8k7a_36936.map" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5732 2.51 5 N 1464 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.26 Number of scatterers: 8918 At special positions: 0 Unit cell: (82.368, 80.652, 141.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1686 8.00 N 1464 7.00 C 5732 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: 0.77 Conformation dependent library (CDL) restraints added in 490.7 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 67.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.322A pdb=" N VAL A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.686A pdb=" N THR A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.430A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.371A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.945A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 4.528A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.973A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 325 removed outlier: 4.309A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 4.540A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.162A pdb=" N ILE A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 416 removed outlier: 3.919A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 444 removed outlier: 3.964A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.767A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.627A pdb=" N ALA A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.759A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.879A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.502A pdb=" N ILE A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 4.339A pdb=" N ALA A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.524A pdb=" N HIS A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.910A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 190 removed outlier: 3.983A pdb=" N ILE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 201 through 251 removed outlier: 3.959A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.186A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 4.053A pdb=" N VAL B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 304 removed outlier: 5.005A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.044A pdb=" N TYR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.078A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.871A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 417 removed outlier: 3.603A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 395 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 396 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.855A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.580A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 532 removed outlier: 4.096A pdb=" N MET B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.510A pdb=" N LEU B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.875A pdb=" N ASN B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 598 removed outlier: 3.652A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.945A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.758A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 removed outlier: 4.300A pdb=" N ALA B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.876A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 5.818A pdb=" N SER A 501 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TYR A 491 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 486 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 542 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A 488 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU A 540 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 561 removed outlier: 6.026A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 672 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 503 removed outlier: 5.935A pdb=" N SER B 501 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR B 491 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 503 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 542 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 561 removed outlier: 5.822A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 643 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 672 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 686 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 699 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1416 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: 1.52 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1709 1.33 - 1.45: 2015 1.45 - 1.57: 5260 1.57 - 1.70: 10 1.70 - 1.82: 56 Bond restraints: 9050 Sorted by residual: bond pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.579 1.672 -0.093 1.10e-02 8.26e+03 7.14e+01 bond pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.579 1.671 -0.092 1.10e-02 8.26e+03 7.01e+01 bond pdb=" C2 ATP A 801 " pdb=" N1 ATP A 801 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C2 ATP B 801 " pdb=" N1 ATP B 801 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.00e-02 1.00e+04 6.49e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.340 0.069 1.00e-02 1.00e+04 4.72e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 11719 2.95 - 5.90: 406 5.90 - 8.85: 100 8.85 - 11.80: 39 11.80 - 14.75: 14 Bond angle restraints: 12278 Sorted by residual: angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 123.40 13.43 1.00e+00 1.00e+00 1.80e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 123.41 13.42 1.00e+00 1.00e+00 1.80e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 127.31 12.56 1.00e+00 1.00e+00 1.58e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 127.34 12.53 1.00e+00 1.00e+00 1.57e+02 angle pdb=" N1 ATP B 801 " pdb=" C2 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 128.69 117.83 10.86 1.00e+00 1.00e+00 1.18e+02 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4874 17.20 - 34.39: 491 34.39 - 51.59: 76 51.59 - 68.79: 8 68.79 - 85.99: 7 Dihedral angle restraints: 5456 sinusoidal: 2162 harmonic: 3294 Sorted by residual: dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU B 444 " pdb=" C LEU B 444 " pdb=" N GLN B 445 " pdb=" CA GLN B 445 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C THR A 613 " pdb=" N THR A 613 " pdb=" CA THR A 613 " pdb=" CB THR A 613 " ideal model delta harmonic sigma weight residual -122.00 -109.05 -12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1409 0.128 - 0.256: 82 0.256 - 0.383: 6 0.383 - 0.511: 0 0.511 - 0.639: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CB ILE A 158 " pdb=" CA ILE A 158 " pdb=" CG1 ILE A 158 " pdb=" CG2 ILE A 158 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 674 " pdb=" CA ILE A 674 " pdb=" CG1 ILE A 674 " pdb=" CG2 ILE A 674 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1495 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 514 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ALA A 514 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA A 514 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A 515 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 331 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C LYS B 331 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 331 " -0.023 2.00e-02 2.50e+03 pdb=" N MET B 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 587 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C THR A 587 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 587 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 588 " -0.016 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 76 2.54 - 3.13: 6510 3.13 - 3.72: 14599 3.72 - 4.31: 19032 4.31 - 4.90: 30072 Nonbonded interactions: 70289 Sorted by model distance: nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 1.952 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.953 2.170 nonbonded pdb=" NE2 GLN A 647 " pdb=" NE2 HIS A 676 " model vdw 2.042 3.200 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.090 2.170 nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 2.090 2.170 ... (remaining 70284 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.080 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.250 Find NCS groups from input model: 0.160 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.208 9051 Z= 0.491 Angle : 1.456 14.748 12278 Z= 0.796 Chirality : 0.067 0.639 1498 Planarity : 0.007 0.076 1522 Dihedral : 13.929 85.987 3332 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.97 % Favored : 93.32 % Rotamer: Outliers : 0.30 % Allowed : 0.91 % Favored : 98.79 % Cbeta Deviations : 0.19 % 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: -3.62 (0.20), residues: 1122 helix: -2.23 (0.16), residues: 672 sheet: -0.22 (1.13), residues: 24 loop : -2.61 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 627 TYR 0.023 0.002 TYR A 384 PHE 0.028 0.002 PHE A 374 TRP 0.013 0.003 TRP B 408 HIS 0.005 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.44 ( 9050) covalent geometry : angle 1.45647 / 0.80 (12278) hydrogen bonds : bond 0.14655 / 9.43 ( 475) hydrogen bonds : angle 6.92546 / 4.75 ( 1416) Misc. bond : bond 0.20807 / 10.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9638 (pt) cc_final: 0.9272 (mm) REVERT: A 526 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 649 THR cc_start: 0.8848 (p) cc_final: 0.8397 (t) REVERT: B 269 PHE cc_start: 0.9310 (t80) cc_final: 0.9099 (t80) REVERT: B 308 PHE cc_start: 0.8864 (t80) cc_final: 0.8593 (t80) REVERT: B 326 MET cc_start: 0.5150 (ptt) cc_final: 0.4269 (ptt) REVERT: B 484 MET cc_start: 0.8908 (tpt) cc_final: 0.8481 (tpp) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.0833 time to fit residues: 17.3413 Evaluate side-chains 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 628 GLN ** B 676 HIS ** 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 = 0.3813 r_free = 0.3813 target = 0.085310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.073302 restraints weight = 70034.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.074878 restraints weight = 42176.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075979 restraints weight = 28600.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.076754 restraints weight = 20977.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.077367 restraints weight = 16335.867| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9051 Z= 0.185 Angle : 0.712 7.344 12278 Z= 0.375 Chirality : 0.042 0.223 1498 Planarity : 0.005 0.044 1522 Dihedral : 5.563 54.123 1218 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.90 % Favored : 94.83 % Rotamer: Outliers : 0.20 % Allowed : 7.68 % Favored : 92.12 % 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: -1.61 (0.23), residues: 1122 helix: -0.51 (0.19), residues: 674 sheet: 0.06 (1.21), residues: 24 loop : -1.95 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 334 TYR 0.016 0.002 TYR A 562 PHE 0.031 0.002 PHE B 309 TRP 0.001 0.000 TRP A 408 HIS 0.007 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 ( 9050) covalent geometry : angle 0.71228 / 0.38 (12278) hydrogen bonds : bond 0.05060 / 3.34 ( 475) hydrogen bonds : angle 4.83327 / 3.33 ( 1416) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.9121 (tmm) cc_final: 0.8803 (tmm) REVERT: A 530 MET cc_start: 0.9263 (mpp) cc_final: 0.9008 (mpp) REVERT: A 607 MET cc_start: 0.7605 (tmm) cc_final: 0.7261 (tmm) REVERT: B 269 PHE cc_start: 0.9808 (t80) cc_final: 0.9524 (t80) REVERT: B 409 MET cc_start: 0.8721 (ppp) cc_final: 0.8358 (ppp) REVERT: B 559 TYR cc_start: 0.9016 (p90) cc_final: 0.8754 (p90) outliers start: 2 outliers final: 2 residues processed: 122 average time/residue: 0.0732 time to fit residues: 13.5343 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN A 628 GLN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 440 ASN B 459 ASN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 GLN B 676 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.043783 restraints weight = 71792.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044938 restraints weight = 52712.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045839 restraints weight = 41606.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.046533 restraints weight = 34498.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047073 restraints weight = 29656.539| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9051 Z= 0.209 Angle : 0.748 8.115 12278 Z= 0.395 Chirality : 0.044 0.212 1498 Planarity : 0.005 0.040 1522 Dihedral : 5.471 42.384 1218 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.24 % Favored : 93.49 % Rotamer: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % 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: -1.16 (0.24), residues: 1122 helix: -0.13 (0.20), residues: 672 sheet: 0.07 (1.22), residues: 24 loop : -1.76 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 593 TYR 0.017 0.002 TYR B 493 PHE 0.032 0.002 PHE B 309 TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 ( 9050) covalent geometry : angle 0.74762 / 0.39 (12278) hydrogen bonds : bond 0.05025 / 3.32 ( 475) hydrogen bonds : angle 4.83832 / 3.33 ( 1416) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 HIS cc_start: 0.9390 (m-70) cc_final: 0.9159 (m170) REVERT: A 310 MET cc_start: 0.4205 (ttt) cc_final: 0.3455 (tpt) REVERT: A 409 MET cc_start: 0.9268 (tmm) cc_final: 0.8755 (ppp) REVERT: A 607 MET cc_start: 0.7937 (tmm) cc_final: 0.7468 (tmm) REVERT: B 196 TYR cc_start: 0.8105 (m-80) cc_final: 0.7877 (m-80) REVERT: B 201 MET cc_start: 0.2557 (mpp) cc_final: 0.2249 (mpp) REVERT: B 269 PHE cc_start: 0.9683 (t80) cc_final: 0.9413 (t80) REVERT: B 308 PHE cc_start: 0.9253 (t80) cc_final: 0.9009 (t80) REVERT: B 310 MET cc_start: 0.5789 (ptp) cc_final: 0.5537 (ptm) REVERT: B 409 MET cc_start: 0.8835 (ppp) cc_final: 0.8465 (ppp) REVERT: B 559 TYR cc_start: 0.8742 (p90) cc_final: 0.8486 (p90) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.0701 time to fit residues: 12.3057 Evaluate side-chains 86 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 628 GLN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.043160 restraints weight = 71403.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.044315 restraints weight = 51967.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.045225 restraints weight = 40793.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.045918 restraints weight = 33642.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.046476 restraints weight = 28813.075| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9051 Z= 0.185 Angle : 0.718 8.954 12278 Z= 0.376 Chirality : 0.044 0.216 1498 Planarity : 0.004 0.041 1522 Dihedral : 5.403 35.181 1218 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.97 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1122 helix: 0.11 (0.20), residues: 666 sheet: 0.10 (1.20), residues: 24 loop : -1.58 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 557 TYR 0.014 0.002 TYR B 493 PHE 0.032 0.002 PHE B 309 TRP 0.006 0.001 TRP B 408 HIS 0.007 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 ( 9050) covalent geometry : angle 0.71833 / 0.38 (12278) hydrogen bonds : bond 0.04978 / 3.29 ( 475) hydrogen bonds : angle 4.72275 / 3.24 ( 1416) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 HIS cc_start: 0.9406 (m-70) cc_final: 0.9171 (m170) REVERT: A 310 MET cc_start: 0.5018 (ttt) cc_final: 0.4204 (tpt) REVERT: A 409 MET cc_start: 0.9280 (tmm) cc_final: 0.8764 (ppp) REVERT: A 442 ILE cc_start: 0.9463 (pt) cc_final: 0.9252 (pt) REVERT: A 607 MET cc_start: 0.7991 (tmm) cc_final: 0.7443 (tmm) REVERT: B 201 MET cc_start: 0.2929 (mpp) cc_final: 0.2662 (mpp) REVERT: B 269 PHE cc_start: 0.9737 (t80) cc_final: 0.9486 (t80) REVERT: B 308 PHE cc_start: 0.9308 (t80) cc_final: 0.9090 (t80) REVERT: B 310 MET cc_start: 0.5857 (ptp) cc_final: 0.5600 (ptm) REVERT: B 357 ILE cc_start: 0.9836 (mp) cc_final: 0.9616 (tp) REVERT: B 409 MET cc_start: 0.8722 (ppp) cc_final: 0.8404 (ppp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0725 time to fit residues: 12.4791 Evaluate side-chains 87 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.056007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045116 restraints weight = 68881.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046287 restraints weight = 51049.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047176 restraints weight = 40459.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.047852 restraints weight = 33573.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048403 restraints weight = 28924.537| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9051 Z= 0.123 Angle : 0.666 9.229 12278 Z= 0.337 Chirality : 0.042 0.186 1498 Planarity : 0.003 0.037 1522 Dihedral : 5.044 37.051 1218 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.90 % Favored : 94.83 % Rotamer: Outliers : 0.20 % Allowed : 3.43 % Favored : 96.36 % 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: -0.52 (0.25), residues: 1122 helix: 0.44 (0.20), residues: 668 sheet: 0.39 (1.19), residues: 24 loop : -1.61 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.009 0.001 TYR A 196 PHE 0.029 0.001 PHE B 309 TRP 0.006 0.001 TRP A 408 HIS 0.009 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9050) covalent geometry : angle 0.66646 / 0.34 (12278) hydrogen bonds : bond 0.04654 / 3.05 ( 475) hydrogen bonds : angle 4.45028 / 3.06 ( 1416) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6607 (mpp) cc_final: 0.6349 (mpp) REVERT: A 308 PHE cc_start: 0.9142 (t80) cc_final: 0.8821 (t80) REVERT: A 310 MET cc_start: 0.4726 (ttt) cc_final: 0.3656 (tpt) REVERT: A 409 MET cc_start: 0.9198 (tmm) cc_final: 0.8687 (ppp) REVERT: A 442 ILE cc_start: 0.9401 (pt) cc_final: 0.9170 (pt) REVERT: A 559 TYR cc_start: 0.8957 (p90) cc_final: 0.8435 (p90) REVERT: A 607 MET cc_start: 0.7936 (tmm) cc_final: 0.7218 (tmm) REVERT: B 269 PHE cc_start: 0.9704 (t80) cc_final: 0.9462 (t80) REVERT: B 308 PHE cc_start: 0.9187 (t80) cc_final: 0.8967 (t80) REVERT: B 310 MET cc_start: 0.5713 (ptp) cc_final: 0.5410 (ptm) REVERT: B 409 MET cc_start: 0.8619 (ppp) cc_final: 0.8325 (ppp) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.0767 time to fit residues: 13.8343 Evaluate side-chains 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.043577 restraints weight = 74422.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044691 restraints weight = 55099.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.045539 restraints weight = 43601.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.046192 restraints weight = 36259.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046722 restraints weight = 31213.563| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9051 Z= 0.174 Angle : 0.710 8.490 12278 Z= 0.368 Chirality : 0.043 0.188 1498 Planarity : 0.004 0.038 1522 Dihedral : 5.210 36.628 1218 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.15 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.25), residues: 1122 helix: 0.34 (0.20), residues: 678 sheet: 0.35 (1.19), residues: 24 loop : -1.58 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 557 TYR 0.012 0.001 TYR A 491 PHE 0.027 0.002 PHE B 309 TRP 0.006 0.001 TRP B 408 HIS 0.008 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 9050) covalent geometry : angle 0.70961 / 0.37 (12278) hydrogen bonds : bond 0.04799 / 3.18 ( 475) hydrogen bonds : angle 4.67944 / 3.22 ( 1416) Misc. bond : bond 0.00079 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.5085 (ttt) cc_final: 0.3950 (ptm) REVERT: A 607 MET cc_start: 0.8014 (tmm) cc_final: 0.7230 (tmm) REVERT: B 269 PHE cc_start: 0.9707 (t80) cc_final: 0.9489 (t80) REVERT: B 308 PHE cc_start: 0.9212 (t80) cc_final: 0.8981 (t80) REVERT: B 310 MET cc_start: 0.6112 (ptp) cc_final: 0.5791 (ptm) REVERT: B 367 TYR cc_start: 0.9353 (t80) cc_final: 0.8726 (t80) REVERT: B 409 MET cc_start: 0.8552 (ppp) cc_final: 0.8347 (ppp) REVERT: B 484 MET cc_start: 0.8984 (tpt) cc_final: 0.8767 (tpt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0713 time to fit residues: 12.8137 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** 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 = 0.3327 r_free = 0.3327 target = 0.056024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044756 restraints weight = 69584.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045922 restraints weight = 51638.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.046844 restraints weight = 41072.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.047567 restraints weight = 34111.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048145 restraints weight = 29339.596| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9051 Z= 0.123 Angle : 0.688 10.585 12278 Z= 0.346 Chirality : 0.043 0.171 1498 Planarity : 0.003 0.039 1522 Dihedral : 4.945 38.085 1218 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.81 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -0.31 (0.25), residues: 1122 helix: 0.58 (0.20), residues: 670 sheet: 0.87 (1.11), residues: 26 loop : -1.50 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.008 0.001 TYR A 196 PHE 0.028 0.001 PHE B 309 TRP 0.007 0.001 TRP A 408 HIS 0.008 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9050) covalent geometry : angle 0.68796 / 0.35 (12278) hydrogen bonds : bond 0.04587 / 3.01 ( 475) hydrogen bonds : angle 4.53008 / 3.12 ( 1416) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.9238 (t80) cc_final: 0.8948 (t80) REVERT: A 310 MET cc_start: 0.4663 (ttt) cc_final: 0.3815 (tpt) REVERT: A 409 MET cc_start: 0.9179 (tmm) cc_final: 0.8731 (ppp) REVERT: A 607 MET cc_start: 0.7889 (tmm) cc_final: 0.7584 (tmm) REVERT: B 196 TYR cc_start: 0.8385 (m-80) cc_final: 0.8044 (m-80) REVERT: B 269 PHE cc_start: 0.9738 (t80) cc_final: 0.9509 (t80) REVERT: B 310 MET cc_start: 0.5921 (ptp) cc_final: 0.5591 (ptm) REVERT: B 367 TYR cc_start: 0.9387 (t80) cc_final: 0.8675 (t80) REVERT: B 419 MET cc_start: 0.7688 (tpt) cc_final: 0.7476 (tpp) REVERT: B 530 MET cc_start: 0.9197 (mpp) cc_final: 0.8904 (mpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0723 time to fit residues: 12.6866 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 46 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 571 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 = 0.3845 r_free = 0.3845 target = 0.086382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.074531 restraints weight = 69577.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.076080 restraints weight = 41206.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.077170 restraints weight = 27534.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.077906 restraints weight = 19839.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.078493 restraints weight = 15209.877| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9051 Z= 0.121 Angle : 0.675 8.159 12278 Z= 0.336 Chirality : 0.042 0.170 1498 Planarity : 0.003 0.038 1522 Dihedral : 4.689 36.681 1218 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.55 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 1.92 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1122 helix: 0.67 (0.21), residues: 670 sheet: 0.83 (1.19), residues: 24 loop : -1.48 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.026 0.001 TYR A 559 PHE 0.024 0.001 PHE B 309 TRP 0.006 0.001 TRP A 408 HIS 0.006 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 9050) covalent geometry : angle 0.67530 / 0.34 (12278) hydrogen bonds : bond 0.04374 / 2.88 ( 475) hydrogen bonds : angle 4.31887 / 2.97 ( 1416) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.9186 (t80) cc_final: 0.8923 (t80) REVERT: A 310 MET cc_start: 0.4204 (ttt) cc_final: 0.3347 (tpt) REVERT: A 409 MET cc_start: 0.9121 (tmm) cc_final: 0.8697 (ppp) REVERT: A 607 MET cc_start: 0.7763 (tmm) cc_final: 0.7464 (tmm) REVERT: A 615 LEU cc_start: 0.9497 (pp) cc_final: 0.9261 (pp) REVERT: B 196 TYR cc_start: 0.7990 (m-80) cc_final: 0.7639 (m-80) REVERT: B 269 PHE cc_start: 0.9679 (t80) cc_final: 0.9439 (t80) REVERT: B 308 PHE cc_start: 0.9051 (t80) cc_final: 0.8772 (t80) REVERT: B 367 TYR cc_start: 0.9341 (t80) cc_final: 0.8945 (t80) REVERT: B 419 MET cc_start: 0.7559 (tpt) cc_final: 0.7324 (tpp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.0740 time to fit residues: 13.4077 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** 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 = 0.3322 r_free = 0.3322 target = 0.056249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.045728 restraints weight = 72088.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.046801 restraints weight = 54843.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047660 restraints weight = 44158.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.048338 restraints weight = 37063.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048758 restraints weight = 31976.434| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9051 Z= 0.140 Angle : 0.712 10.613 12278 Z= 0.364 Chirality : 0.043 0.174 1498 Planarity : 0.004 0.037 1522 Dihedral : 4.755 33.638 1218 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.17 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1122 helix: 0.52 (0.20), residues: 684 sheet: 0.78 (1.19), residues: 24 loop : -1.51 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.022 0.001 TYR A 559 PHE 0.025 0.001 PHE B 309 TRP 0.004 0.001 TRP B 408 HIS 0.007 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9050) covalent geometry : angle 0.71234 / 0.36 (12278) hydrogen bonds : bond 0.04390 / 2.89 ( 475) hydrogen bonds : angle 4.53075 / 3.12 ( 1416) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4430 (ttt) cc_final: 0.3387 (ptm) REVERT: A 607 MET cc_start: 0.7953 (tmm) cc_final: 0.7645 (tmm) REVERT: B 196 TYR cc_start: 0.8345 (m-80) cc_final: 0.7976 (m-80) REVERT: B 269 PHE cc_start: 0.9716 (t80) cc_final: 0.9499 (t80) REVERT: B 308 PHE cc_start: 0.9124 (t80) cc_final: 0.8848 (t80) REVERT: B 367 TYR cc_start: 0.9375 (t80) cc_final: 0.8770 (t80) REVERT: B 530 MET cc_start: 0.9174 (mpp) cc_final: 0.8902 (mpp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0739 time to fit residues: 12.9414 Evaluate side-chains 87 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0370 chunk 31 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045902 restraints weight = 69135.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047006 restraints weight = 52249.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047865 restraints weight = 41911.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048559 restraints weight = 35073.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049120 restraints weight = 30171.994| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9051 Z= 0.128 Angle : 0.710 10.247 12278 Z= 0.359 Chirality : 0.043 0.175 1498 Planarity : 0.003 0.038 1522 Dihedral : 4.746 34.894 1218 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.99 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1122 helix: 0.56 (0.20), residues: 680 sheet: 0.80 (1.18), residues: 24 loop : -1.48 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.023 0.001 TYR A 559 PHE 0.027 0.001 PHE B 309 TRP 0.004 0.001 TRP A 408 HIS 0.006 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 9050) covalent geometry : angle 0.71044 / 0.36 (12278) hydrogen bonds : bond 0.04347 / 2.84 ( 475) hydrogen bonds : angle 4.46368 / 3.07 ( 1416) Misc. bond : bond 0.00019 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.9237 (t80) cc_final: 0.8944 (t80) REVERT: A 310 MET cc_start: 0.4351 (ttt) cc_final: 0.3289 (ptm) REVERT: A 500 LEU cc_start: 0.9137 (tp) cc_final: 0.8918 (tt) REVERT: A 607 MET cc_start: 0.7811 (tmm) cc_final: 0.7515 (tmm) REVERT: B 196 TYR cc_start: 0.8353 (m-80) cc_final: 0.7972 (m-80) REVERT: B 269 PHE cc_start: 0.9702 (t80) cc_final: 0.9489 (t80) REVERT: B 308 PHE cc_start: 0.9104 (t80) cc_final: 0.8831 (t80) REVERT: B 367 TYR cc_start: 0.9362 (t80) cc_final: 0.8778 (t80) REVERT: B 409 MET cc_start: 0.8479 (ppp) cc_final: 0.8262 (ppp) REVERT: B 530 MET cc_start: 0.9211 (mpp) cc_final: 0.8898 (mpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0787 time to fit residues: 13.3673 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 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 = 0.3739 r_free = 0.3739 target = 0.080125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.068788 restraints weight = 71909.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.070251 restraints weight = 42260.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071255 restraints weight = 28351.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.071933 restraints weight = 20630.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.072426 restraints weight = 15963.050| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9051 Z= 0.182 Angle : 0.755 10.859 12278 Z= 0.390 Chirality : 0.044 0.186 1498 Planarity : 0.004 0.053 1522 Dihedral : 5.139 37.488 1218 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1122 helix: 0.49 (0.20), residues: 676 sheet: 0.93 (1.10), residues: 26 loop : -1.45 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 557 TYR 0.022 0.001 TYR A 559 PHE 0.028 0.002 PHE B 309 TRP 0.005 0.001 TRP B 408 HIS 0.008 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 9050) covalent geometry : angle 0.75532 / 0.39 (12278) hydrogen bonds : bond 0.04652 / 3.05 ( 475) hydrogen bonds : angle 4.74940 / 3.27 ( 1416) Misc. bond : bond 0.00087 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.32 seconds wall clock time: 26 minutes 2.52 seconds (1562.52 seconds total)