Starting phenix.real_space_refine on Sat Dec 28 20:40:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_36936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_36936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_36936.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_36936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7a_36936/12_2024/8k7a_36936.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.53, per 1000 atoms: 0.62 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 2.53 Time building geometry restraints manager: 2.57 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: 4896 17.20 - 34.39: 495 34.39 - 51.59: 100 51.59 - 68.79: 20 68.79 - 85.99: 7 Dihedral angle restraints: 5518 sinusoidal: 2224 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 5515 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: 0.00 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 0.093 9050 Z= 0.432 Angle : 1.456 14.748 12278 Z= 0.796 Chirality : 0.067 0.639 1498 Planarity : 0.007 0.076 1522 Dihedral : 14.726 85.987 3394 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (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 TRP 0.013 0.003 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.028 0.002 PHE A 374 TYR 0.023 0.002 TYR A 384 ARG 0.018 0.001 ARG B 627 *********************** 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 : 1.065 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: 0.1808 time to fit residues: 37.0658 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 : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.0170 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9050 Z= 0.143 Angle : 0.670 7.210 12278 Z= 0.340 Chirality : 0.041 0.227 1498 Planarity : 0.004 0.046 1522 Dihedral : 8.481 75.048 1280 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.28 % Favored : 95.45 % Rotamer: Outliers : 0.10 % Allowed : 6.57 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1122 helix: -0.64 (0.19), residues: 678 sheet: -0.01 (1.18), residues: 24 loop : -2.10 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 408 HIS 0.004 0.001 HIS A 490 PHE 0.031 0.001 PHE B 309 TYR 0.012 0.001 TYR A 559 ARG 0.005 0.000 ARG B 627 *********************** 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 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASN cc_start: 0.9696 (t0) cc_final: 0.9484 (t0) REVERT: A 607 MET cc_start: 0.7632 (tmm) cc_final: 0.7335 (tmm) REVERT: B 308 PHE cc_start: 0.8860 (t80) cc_final: 0.8531 (t80) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1718 time to fit residues: 32.8736 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.185 Angle : 0.666 7.007 12278 Z= 0.344 Chirality : 0.041 0.184 1498 Planarity : 0.004 0.042 1522 Dihedral : 8.221 87.992 1280 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 0.20 % Allowed : 4.85 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1122 helix: -0.07 (0.20), residues: 674 sheet: 0.35 (1.24), residues: 24 loop : -1.85 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.028 0.002 PHE B 309 TYR 0.017 0.001 TYR A 493 ARG 0.004 0.000 ARG B 627 *********************** 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 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9640 (pt) cc_final: 0.9306 (mm) REVERT: A 310 MET cc_start: 0.3690 (ttt) cc_final: 0.3040 (tpt) REVERT: A 409 MET cc_start: 0.9054 (tmm) cc_final: 0.8769 (ppp) REVERT: A 607 MET cc_start: 0.7861 (tmm) cc_final: 0.7371 (tmm) REVERT: B 269 PHE cc_start: 0.9414 (t80) cc_final: 0.9209 (t80) REVERT: B 310 MET cc_start: 0.5192 (ptp) cc_final: 0.4955 (ptm) REVERT: B 357 ILE cc_start: 0.9780 (mm) cc_final: 0.9548 (tp) REVERT: B 409 MET cc_start: 0.8767 (ppp) cc_final: 0.8378 (ppp) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1613 time to fit residues: 28.8769 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 440 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9050 Z= 0.202 Angle : 0.673 8.399 12278 Z= 0.348 Chirality : 0.042 0.193 1498 Planarity : 0.004 0.038 1522 Dihedral : 7.530 84.547 1280 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.88 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1122 helix: 0.24 (0.20), residues: 668 sheet: 0.32 (1.24), residues: 24 loop : -1.62 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.029 0.002 PHE B 309 TYR 0.020 0.001 TYR A 559 ARG 0.004 0.001 ARG A 557 *********************** 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 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9642 (pt) cc_final: 0.9310 (mm) REVERT: A 310 MET cc_start: 0.4449 (ttt) cc_final: 0.3576 (tpt) REVERT: A 409 MET cc_start: 0.9142 (tmm) cc_final: 0.8815 (ppp) REVERT: A 607 MET cc_start: 0.7971 (tmm) cc_final: 0.7253 (tmm) REVERT: B 196 TYR cc_start: 0.8131 (m-80) cc_final: 0.7728 (m-80) REVERT: B 229 LEU cc_start: 0.9701 (mm) cc_final: 0.9442 (pp) REVERT: B 269 PHE cc_start: 0.9442 (t80) cc_final: 0.9228 (t80) REVERT: B 308 PHE cc_start: 0.8932 (t80) cc_final: 0.8714 (t80) REVERT: B 310 MET cc_start: 0.5642 (ptp) cc_final: 0.5352 (ptm) REVERT: B 357 ILE cc_start: 0.9787 (mm) cc_final: 0.9550 (tp) REVERT: B 409 MET cc_start: 0.8739 (ppp) cc_final: 0.8397 (ppp) REVERT: B 484 MET cc_start: 0.8884 (tpt) cc_final: 0.8327 (tpp) REVERT: B 690 LEU cc_start: 0.9344 (tp) cc_final: 0.8878 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1674 time to fit residues: 29.5167 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.0170 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9050 Z= 0.149 Angle : 0.648 8.077 12278 Z= 0.328 Chirality : 0.041 0.184 1498 Planarity : 0.003 0.035 1522 Dihedral : 6.867 84.411 1280 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.90 % Favored : 94.83 % Rotamer: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1122 helix: 0.50 (0.21), residues: 670 sheet: 0.50 (1.21), residues: 24 loop : -1.53 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.006 0.001 HIS A 490 PHE 0.028 0.001 PHE B 309 TYR 0.010 0.001 TYR A 493 ARG 0.002 0.000 ARG B 334 *********************** 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 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4291 (ttt) cc_final: 0.3349 (tpt) REVERT: A 409 MET cc_start: 0.9093 (tmm) cc_final: 0.8757 (ppp) REVERT: A 607 MET cc_start: 0.7904 (tmm) cc_final: 0.7104 (tmm) REVERT: B 196 TYR cc_start: 0.8044 (m-80) cc_final: 0.7705 (m-80) REVERT: B 269 PHE cc_start: 0.9433 (t80) cc_final: 0.9229 (t80) REVERT: B 310 MET cc_start: 0.5474 (ptp) cc_final: 0.5175 (ptm) REVERT: B 357 ILE cc_start: 0.9772 (mm) cc_final: 0.9517 (tp) REVERT: B 409 MET cc_start: 0.8616 (ppp) cc_final: 0.8298 (ppp) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.1616 time to fit residues: 30.0441 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 : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9050 Z= 0.154 Angle : 0.667 8.845 12278 Z= 0.339 Chirality : 0.042 0.196 1498 Planarity : 0.003 0.034 1522 Dihedral : 6.577 87.351 1280 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.26 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1122 helix: 0.53 (0.20), residues: 670 sheet: 0.67 (1.21), residues: 24 loop : -1.47 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.026 0.001 PHE B 309 TYR 0.023 0.001 TYR A 559 ARG 0.002 0.000 ARG A 557 *********************** 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 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.9141 (mp0) cc_final: 0.8907 (pm20) REVERT: A 310 MET cc_start: 0.4261 (ttt) cc_final: 0.3156 (tpt) REVERT: A 409 MET cc_start: 0.9105 (tmm) cc_final: 0.8761 (ppp) REVERT: A 607 MET cc_start: 0.7873 (tmm) cc_final: 0.7601 (tmm) REVERT: B 196 TYR cc_start: 0.8108 (m-80) cc_final: 0.7799 (m-80) REVERT: B 308 PHE cc_start: 0.8796 (t80) cc_final: 0.8547 (t80) REVERT: B 310 MET cc_start: 0.5068 (ptp) cc_final: 0.4825 (ptm) REVERT: B 357 ILE cc_start: 0.9767 (mm) cc_final: 0.9468 (tp) REVERT: B 367 TYR cc_start: 0.9238 (t80) cc_final: 0.8635 (t80) REVERT: B 409 MET cc_start: 0.8502 (ppp) cc_final: 0.8259 (ppp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1623 time to fit residues: 28.7131 Evaluate side-chains 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 248 HIS B 459 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9050 Z= 0.204 Angle : 0.700 8.641 12278 Z= 0.362 Chirality : 0.043 0.187 1498 Planarity : 0.004 0.043 1522 Dihedral : 6.702 85.146 1280 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.70 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1122 helix: 0.51 (0.20), residues: 670 sheet: 0.55 (1.18), residues: 24 loop : -1.48 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.006 0.001 HIS A 490 PHE 0.028 0.002 PHE B 309 TYR 0.019 0.001 TYR A 493 ARG 0.003 0.000 ARG B 677 *********************** 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 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4619 (ttt) cc_final: 0.3623 (tpt) REVERT: A 357 ILE cc_start: 0.9715 (mp) cc_final: 0.9277 (tp) REVERT: A 409 MET cc_start: 0.9222 (tmm) cc_final: 0.8878 (ppp) REVERT: A 607 MET cc_start: 0.7997 (tmm) cc_final: 0.7711 (tmm) REVERT: B 201 MET cc_start: 0.3190 (mpp) cc_final: 0.2809 (mpp) REVERT: B 308 PHE cc_start: 0.8869 (t80) cc_final: 0.8661 (t80) REVERT: B 310 MET cc_start: 0.5323 (ptp) cc_final: 0.5005 (ptm) REVERT: B 357 ILE cc_start: 0.9787 (mm) cc_final: 0.9502 (tp) REVERT: B 367 TYR cc_start: 0.9286 (t80) cc_final: 0.9000 (t80) REVERT: B 409 MET cc_start: 0.8544 (ppp) cc_final: 0.8332 (ppp) REVERT: B 607 MET cc_start: 0.7183 (tmm) cc_final: 0.6937 (tmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1629 time to fit residues: 27.9602 Evaluate side-chains 88 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.166 Angle : 0.681 10.184 12278 Z= 0.349 Chirality : 0.043 0.202 1498 Planarity : 0.004 0.037 1522 Dihedral : 6.641 86.429 1280 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1122 helix: 0.64 (0.20), residues: 672 sheet: 0.71 (1.19), residues: 24 loop : -1.43 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.006 0.001 HIS A 490 PHE 0.029 0.001 PHE B 309 TYR 0.024 0.001 TYR A 559 ARG 0.002 0.000 ARG B 457 *********************** 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4491 (ttt) cc_final: 0.3475 (tpt) REVERT: A 404 VAL cc_start: 0.8855 (m) cc_final: 0.8611 (p) REVERT: A 409 MET cc_start: 0.9192 (tmm) cc_final: 0.8959 (tmm) REVERT: A 607 MET cc_start: 0.7934 (tmm) cc_final: 0.7638 (tmm) REVERT: B 201 MET cc_start: 0.3200 (mpp) cc_final: 0.2818 (mpp) REVERT: B 310 MET cc_start: 0.5137 (ptp) cc_final: 0.4857 (ptm) REVERT: B 357 ILE cc_start: 0.9781 (mm) cc_final: 0.9484 (tp) REVERT: B 367 TYR cc_start: 0.9248 (t80) cc_final: 0.8954 (t80) REVERT: B 409 MET cc_start: 0.8519 (ppp) cc_final: 0.8305 (ppp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1604 time to fit residues: 27.6766 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 : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.150 Angle : 0.702 10.081 12278 Z= 0.352 Chirality : 0.043 0.179 1498 Planarity : 0.003 0.038 1522 Dihedral : 6.509 85.918 1280 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.55 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 0.71 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1122 helix: 0.66 (0.21), residues: 672 sheet: 0.85 (1.19), residues: 24 loop : -1.37 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.009 0.001 HIS A 490 PHE 0.028 0.001 PHE B 309 TYR 0.014 0.001 TYR A 559 ARG 0.002 0.000 ARG B 260 *********************** 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.9293 (mp0) cc_final: 0.9016 (pm20) REVERT: A 310 MET cc_start: 0.4124 (ttt) cc_final: 0.2875 (ptm) REVERT: A 404 VAL cc_start: 0.8795 (m) cc_final: 0.8560 (p) REVERT: A 607 MET cc_start: 0.7889 (tmm) cc_final: 0.7573 (tmm) REVERT: B 310 MET cc_start: 0.5043 (ptp) cc_final: 0.4826 (ptm) REVERT: B 357 ILE cc_start: 0.9763 (mm) cc_final: 0.9444 (tp) REVERT: B 367 TYR cc_start: 0.9190 (t80) cc_final: 0.8885 (t80) REVERT: B 384 TYR cc_start: 0.9123 (t80) cc_final: 0.8896 (t80) REVERT: B 409 MET cc_start: 0.8450 (ppp) cc_final: 0.8243 (ppp) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1671 time to fit residues: 28.6600 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 : 1.089 ------------------------------------------------------------------------------- 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: 0.0980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.0670 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9050 Z= 0.147 Angle : 0.699 10.546 12278 Z= 0.346 Chirality : 0.043 0.176 1498 Planarity : 0.003 0.038 1522 Dihedral : 6.364 84.491 1280 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.19 % Favored : 95.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1122 helix: 0.69 (0.21), residues: 672 sheet: 0.95 (1.19), residues: 24 loop : -1.40 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.008 0.001 HIS A 490 PHE 0.027 0.001 PHE B 309 TYR 0.023 0.001 TYR A 559 ARG 0.002 0.000 ARG B 260 ********************** 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 113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.3931 (ttt) cc_final: 0.2712 (ptm) REVERT: A 404 VAL cc_start: 0.8713 (m) cc_final: 0.8485 (p) REVERT: A 607 MET cc_start: 0.7731 (tmm) cc_final: 0.7413 (tmm) REVERT: A 615 LEU cc_start: 0.9463 (pp) cc_final: 0.9232 (pp) REVERT: B 357 ILE cc_start: 0.9732 (mm) cc_final: 0.9412 (tp) REVERT: B 367 TYR cc_start: 0.9152 (t80) cc_final: 0.8830 (t80) REVERT: B 384 TYR cc_start: 0.9088 (t80) cc_final: 0.8713 (t80) REVERT: B 409 MET cc_start: 0.8417 (ppp) cc_final: 0.8186 (ppp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1597 time to fit residues: 27.7302 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 : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.089055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.076944 restraints weight = 68044.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.078510 restraints weight = 40531.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.079584 restraints weight = 27269.890| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9050 Z= 0.144 Angle : 0.695 10.108 12278 Z= 0.344 Chirality : 0.043 0.173 1498 Planarity : 0.003 0.037 1522 Dihedral : 6.260 82.908 1280 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.01 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1122 helix: 0.71 (0.21), residues: 672 sheet: 1.05 (1.19), residues: 24 loop : -1.39 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.008 0.001 HIS A 490 PHE 0.027 0.001 PHE B 309 TYR 0.014 0.001 TYR A 559 ARG 0.002 0.000 ARG B 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.78 seconds wall clock time: 31 minutes 39.33 seconds (1899.33 seconds total)