Starting phenix.real_space_refine on Sun May 3 06:06:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.map" model { file = "/net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwn_74913/05_2026/9zwn_74913.cif" } resolution = 2.58 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= 0.028 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 K 3 8.98 5 P 3 5.49 5 S 62 5.16 5 C 7012 2.51 5 N 1817 2.21 5 O 2017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10914 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4156 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 4981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 4981 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 25, 'TRANS': 645} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1414 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {' K': 1, '9Y0': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10914 At special positions: 0 Unit cell: (137.64, 101.37, 129.27, 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) K 3 19.00 S 62 16.00 P 3 15.00 O 2017 8.00 N 1817 7.00 C 7012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 503.4 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 9 sheets defined 64.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.711A pdb=" N MET A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.601A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.561A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.555A pdb=" N THR A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.577A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.881A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 275 removed outlier: 3.623A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.784A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.405A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.379A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.898A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 4.125A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix removed outlier: 3.698A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.791A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 436 removed outlier: 4.672A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.680A pdb=" N MET A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.697A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.979A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 508 removed outlier: 4.723A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.194A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.674A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.581A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.952A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 88 removed outlier: 3.524A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.670A pdb=" N SER B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.548A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 removed outlier: 4.087A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 removed outlier: 4.194A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.814A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.731A pdb=" N ALA B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 removed outlier: 4.327A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.765A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.966A pdb=" N PHE B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.713A pdb=" N ARG B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.577A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.526A pdb=" N ALA B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.632A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.670A pdb=" N GLY B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 588 removed outlier: 3.539A pdb=" N GLN B 567 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.548A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.664A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.652A pdb=" N ARG B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 662 Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.715A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 671 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 672 " --> pdb=" O GLY B 668 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.865A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.771A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.689A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 removed outlier: 3.685A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'D' and resid 26 through 29 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.598A pdb=" N GLY B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.145A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 324 removed outlier: 7.023A pdb=" N ASN B 316 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 448 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 440 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.913A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.622A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1746 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: 1.88 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1906 1.33 - 1.45: 2613 1.45 - 1.57: 6424 1.57 - 1.69: 4 1.69 - 1.81: 113 Bond restraints: 11060 Sorted by residual: bond pdb=" C PHD B 307 " pdb=" O PHD B 307 " ideal model delta sigma weight residual 1.231 1.268 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" CA PHD B 307 " pdb=" C PHD B 307 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.60e+00 bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.784 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" CG PHD B 307 " pdb=" OD2 PHD B 307 " ideal model delta sigma weight residual 1.218 1.249 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" CB ASN C 149 " pdb=" CG ASN C 149 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.73e+00 ... (remaining 11055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14860 1.84 - 3.68: 133 3.68 - 5.52: 27 5.52 - 7.36: 7 7.36 - 9.19: 3 Bond angle restraints: 15030 Sorted by residual: angle pdb=" N ILE B 267 " pdb=" CA ILE B 267 " pdb=" C ILE B 267 " ideal model delta sigma weight residual 113.53 108.78 4.75 9.80e-01 1.04e+00 2.35e+01 angle pdb=" C ALA B 285 " pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.15e+00 angle pdb=" CA LEU B 440 " pdb=" CB LEU B 440 " pdb=" CG LEU B 440 " ideal model delta sigma weight residual 116.30 125.49 -9.19 3.50e+00 8.16e-02 6.90e+00 angle pdb=" CB ARG B 511 " pdb=" CG ARG B 511 " pdb=" CD ARG B 511 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.72e+00 angle pdb=" CA ASN C 149 " pdb=" CB ASN C 149 " pdb=" CG ASN C 149 " ideal model delta sigma weight residual 112.60 115.18 -2.58 1.00e+00 1.00e+00 6.67e+00 ... (remaining 15025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 6103 27.04 - 54.07: 444 54.07 - 81.11: 49 81.11 - 108.14: 6 108.14 - 135.18: 2 Dihedral angle restraints: 6604 sinusoidal: 2513 harmonic: 4091 Sorted by residual: dihedral pdb=" CB CYS B 142 " pdb=" SG CYS B 142 " pdb=" SG CYS B 191 " pdb=" CB CYS B 191 " ideal model delta sinusoidal sigma weight residual 93.00 156.61 -63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" C23 9Y0 B 702 " pdb=" C21 9Y0 B 702 " pdb=" C22 9Y0 B 702 " pdb=" O7 9Y0 B 702 " ideal model delta sinusoidal sigma weight residual 181.02 45.84 135.18 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C23 9Y0 B 702 " pdb=" C21 9Y0 B 702 " pdb=" C22 9Y0 B 702 " pdb=" O6 9Y0 B 702 " ideal model delta sinusoidal sigma weight residual 0.61 -134.03 134.64 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 6601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1206 0.028 - 0.057: 388 0.057 - 0.085: 125 0.085 - 0.114: 74 0.114 - 0.142: 9 Chirality restraints: 1802 Sorted by residual: chirality pdb=" CA ASN B 286 " pdb=" N ASN B 286 " pdb=" C ASN B 286 " pdb=" CB ASN B 286 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL B 193 " pdb=" N VAL B 193 " pdb=" C VAL B 193 " pdb=" CB VAL B 193 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1799 not shown) Planarity restraints: 1899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 149 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ASN C 149 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN C 149 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 150 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO B 496 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO C 110 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.027 5.00e-02 4.00e+02 ... (remaining 1896 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2290 2.78 - 3.37: 12456 3.37 - 3.96: 21572 3.96 - 4.55: 30332 4.55 - 5.14: 43117 Nonbonded interactions: 109767 Sorted by model distance: nonbonded pdb=" OE1 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.187 3.040 nonbonded pdb=" O GLN A 304 " pdb=" OG SER A 317 " model vdw 2.201 3.040 nonbonded pdb=" O ALA A 238 " pdb=" OG SER A 241 " model vdw 2.217 3.040 nonbonded pdb=" O ARG B 572 " pdb=" OG1 THR B 576 " model vdw 2.239 3.040 nonbonded pdb=" O PHD B 307 " pdb=" OG1 THR B 311 " model vdw 2.240 3.040 ... (remaining 109762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.002 0.050 11061 Z= 0.088 Angle : 0.475 9.195 15032 Z= 0.233 Chirality : 0.036 0.142 1802 Planarity : 0.003 0.053 1899 Dihedral : 17.625 135.180 3973 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 26.28 % Favored : 71.06 % 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: 0.22 (0.22), residues: 1434 helix: 0.84 (0.18), residues: 828 sheet: 0.93 (0.60), residues: 86 loop : -1.06 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.014 0.001 TYR C 170 PHE 0.004 0.000 PHE B 374 TRP 0.007 0.000 TRP C 139 HIS 0.001 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00187 (11060) covalent geometry : angle 0.47454 (15030) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.32590 ( 2) hydrogen bonds : bond 0.25892 ( 606) hydrogen bonds : angle 7.11938 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 28 residues processed: 147 average time/residue: 0.4941 time to fit residues: 79.7082 Evaluate side-chains 144 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.188135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108330 restraints weight = 12179.875| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.63 r_work: 0.3146 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11061 Z= 0.172 Angle : 0.563 7.370 15032 Z= 0.290 Chirality : 0.042 0.163 1802 Planarity : 0.004 0.048 1899 Dihedral : 9.876 120.924 1640 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.89 % Allowed : 22.57 % Favored : 73.54 % 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: 0.18 (0.21), residues: 1434 helix: 0.82 (0.17), residues: 872 sheet: 1.01 (0.63), residues: 75 loop : -1.26 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.025 0.002 TYR A 381 PHE 0.018 0.002 PHE A 109 TRP 0.012 0.001 TRP A 115 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00392 (11060) covalent geometry : angle 0.56284 (15030) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.73508 ( 2) hydrogen bonds : bond 0.05658 ( 606) hydrogen bonds : angle 4.68632 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7145 (mtmt) REVERT: A 357 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8657 (tp) REVERT: B 261 CYS cc_start: 0.7514 (m) cc_final: 0.7242 (m) REVERT: B 535 MET cc_start: 0.7164 (mmt) cc_final: 0.5681 (mmm) REVERT: C 149 ASN cc_start: 0.8507 (t0) cc_final: 0.8190 (t0) outliers start: 44 outliers final: 18 residues processed: 155 average time/residue: 0.5365 time to fit residues: 90.3816 Evaluate side-chains 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 40.0000 chunk 123 optimal weight: 0.8980 chunk 92 optimal weight: 40.0000 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 133 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 130 ASN C 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.188155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108223 restraints weight = 12216.671| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.65 r_work: 0.3139 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11061 Z= 0.119 Angle : 0.502 7.174 15032 Z= 0.252 Chirality : 0.039 0.170 1802 Planarity : 0.004 0.066 1899 Dihedral : 9.518 111.147 1616 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.01 % Allowed : 23.63 % Favored : 73.36 % 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: 0.47 (0.22), residues: 1434 helix: 1.12 (0.18), residues: 872 sheet: 1.05 (0.63), residues: 75 loop : -1.27 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 511 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 109 TRP 0.015 0.001 TRP B 245 HIS 0.002 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00266 (11060) covalent geometry : angle 0.50164 (15030) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.46243 ( 2) hydrogen bonds : bond 0.04577 ( 606) hydrogen bonds : angle 4.25328 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7765 (ttp-170) REVERT: A 55 ARG cc_start: 0.7632 (tmm160) cc_final: 0.7388 (tmm160) REVERT: A 60 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7253 (mtmt) REVERT: B 383 MET cc_start: 0.5686 (mtt) cc_final: 0.5147 (mmt) REVERT: B 392 MET cc_start: 0.3706 (ppp) cc_final: 0.3004 (ppp) REVERT: B 422 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6926 (tm-30) REVERT: B 466 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6729 (tmmm) REVERT: B 535 MET cc_start: 0.7221 (mmt) cc_final: 0.5758 (mmm) REVERT: C 149 ASN cc_start: 0.8502 (t0) cc_final: 0.8133 (t0) REVERT: C 169 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7924 (tptt) outliers start: 34 outliers final: 11 residues processed: 154 average time/residue: 0.5876 time to fit residues: 97.7821 Evaluate side-chains 133 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 611 HIS C 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103138 restraints weight = 12287.581| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.65 r_work: 0.3049 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11061 Z= 0.169 Angle : 0.550 6.769 15032 Z= 0.277 Chirality : 0.041 0.182 1802 Planarity : 0.004 0.048 1899 Dihedral : 9.567 105.161 1611 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.07 % Allowed : 22.92 % Favored : 73.01 % 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: 0.27 (0.22), residues: 1434 helix: 0.95 (0.17), residues: 877 sheet: 0.99 (0.61), residues: 79 loop : -1.37 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 511 TYR 0.025 0.002 TYR A 381 PHE 0.014 0.001 PHE A 109 TRP 0.019 0.001 TRP B 245 HIS 0.005 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00403 (11060) covalent geometry : angle 0.54975 (15030) SS BOND : bond 0.00569 ( 1) SS BOND : angle 0.10885 ( 2) hydrogen bonds : bond 0.04908 ( 606) hydrogen bonds : angle 4.34486 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.422 Fit side-chains REVERT: A 48 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7727 (ttp-170) REVERT: A 60 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7311 (mtmt) REVERT: B 383 MET cc_start: 0.5657 (mtt) cc_final: 0.5165 (mmt) REVERT: B 422 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7037 (tm-30) REVERT: B 435 GLU cc_start: 0.4314 (OUTLIER) cc_final: 0.3511 (tp30) REVERT: B 466 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6606 (tmmm) REVERT: C 149 ASN cc_start: 0.8540 (t0) cc_final: 0.8160 (t0) REVERT: C 164 GLN cc_start: 0.7585 (mt0) cc_final: 0.7230 (mp10) outliers start: 46 outliers final: 20 residues processed: 153 average time/residue: 0.5504 time to fit residues: 91.6159 Evaluate side-chains 145 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.186616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105978 restraints weight = 12186.622| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.62 r_work: 0.3106 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11061 Z= 0.112 Angle : 0.499 7.561 15032 Z= 0.251 Chirality : 0.039 0.178 1802 Planarity : 0.004 0.050 1899 Dihedral : 9.212 94.726 1609 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.63 % Allowed : 23.19 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.22), residues: 1434 helix: 1.18 (0.17), residues: 879 sheet: 0.99 (0.61), residues: 75 loop : -1.33 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE A 527 TRP 0.012 0.001 TRP B 245 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00251 (11060) covalent geometry : angle 0.49938 (15030) SS BOND : bond 0.00301 ( 1) SS BOND : angle 0.48304 ( 2) hydrogen bonds : bond 0.04055 ( 606) hydrogen bonds : angle 4.12872 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.419 Fit side-chains REVERT: A 357 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 45 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6597 (mp) REVERT: B 383 MET cc_start: 0.5588 (mtt) cc_final: 0.5100 (mmt) REVERT: B 422 GLN cc_start: 0.7303 (mm-40) cc_final: 0.7030 (tm-30) REVERT: B 435 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.3458 (tp30) REVERT: B 466 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6583 (tmmm) REVERT: C 149 ASN cc_start: 0.8543 (t0) cc_final: 0.8162 (t0) REVERT: C 164 GLN cc_start: 0.7557 (mt0) cc_final: 0.7162 (mp10) outliers start: 41 outliers final: 19 residues processed: 151 average time/residue: 0.5522 time to fit residues: 90.6252 Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 27 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 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 = 0.4154 r_free = 0.4154 target = 0.185370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104513 restraints weight = 12324.244| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.64 r_work: 0.3084 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11061 Z= 0.134 Angle : 0.512 7.716 15032 Z= 0.258 Chirality : 0.040 0.179 1802 Planarity : 0.004 0.050 1899 Dihedral : 8.968 86.191 1609 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.07 % Allowed : 22.83 % Favored : 73.10 % 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 (0.22), residues: 1434 helix: 1.16 (0.17), residues: 880 sheet: 0.71 (0.59), residues: 85 loop : -1.24 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 21 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.010 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00316 (11060) covalent geometry : angle 0.51222 (15030) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.49325 ( 2) hydrogen bonds : bond 0.04276 ( 606) hydrogen bonds : angle 4.13730 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.389 Fit side-chains REVERT: A 48 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7677 (ttp-110) REVERT: A 60 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7227 (mtmt) REVERT: A 357 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8270 (mp) REVERT: B 45 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6656 (mp) REVERT: B 383 MET cc_start: 0.5591 (mtt) cc_final: 0.5154 (mmt) REVERT: B 422 GLN cc_start: 0.7317 (mm-40) cc_final: 0.6994 (tm-30) REVERT: B 435 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3651 (tp30) REVERT: C 149 ASN cc_start: 0.8522 (t0) cc_final: 0.8136 (t0) REVERT: C 164 GLN cc_start: 0.7553 (mt0) cc_final: 0.7159 (mp10) outliers start: 46 outliers final: 23 residues processed: 152 average time/residue: 0.6020 time to fit residues: 98.7024 Evaluate side-chains 147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.185968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105199 restraints weight = 12187.893| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.63 r_work: 0.3094 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11061 Z= 0.123 Angle : 0.514 7.958 15032 Z= 0.258 Chirality : 0.040 0.178 1802 Planarity : 0.004 0.050 1899 Dihedral : 8.701 85.411 1609 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.01 % Allowed : 23.45 % Favored : 73.54 % 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 (0.22), residues: 1434 helix: 1.23 (0.17), residues: 880 sheet: 0.63 (0.59), residues: 85 loop : -1.27 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 391 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.010 0.001 TRP B 245 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00287 (11060) covalent geometry : angle 0.51411 (15030) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.49350 ( 2) hydrogen bonds : bond 0.04076 ( 606) hydrogen bonds : angle 4.07318 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.414 Fit side-chains REVERT: A 60 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7244 (mtmt) REVERT: A 357 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 45 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6571 (mp) REVERT: B 383 MET cc_start: 0.5466 (mtt) cc_final: 0.5039 (mmt) REVERT: B 422 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7046 (tm-30) REVERT: B 435 GLU cc_start: 0.4336 (OUTLIER) cc_final: 0.3980 (tp30) REVERT: C 149 ASN cc_start: 0.8542 (t0) cc_final: 0.8136 (t0) REVERT: C 164 GLN cc_start: 0.7477 (mt0) cc_final: 0.7092 (mp10) REVERT: C 187 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7677 (pttm) outliers start: 34 outliers final: 21 residues processed: 148 average time/residue: 0.6105 time to fit residues: 97.4498 Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103863 restraints weight = 12232.803| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.63 r_work: 0.3057 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11061 Z= 0.147 Angle : 0.530 8.292 15032 Z= 0.266 Chirality : 0.041 0.175 1802 Planarity : 0.004 0.050 1899 Dihedral : 8.690 87.156 1609 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.10 % Allowed : 23.72 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.22), residues: 1434 helix: 1.16 (0.17), residues: 881 sheet: 0.89 (0.62), residues: 75 loop : -1.33 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.023 0.002 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.009 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00350 (11060) covalent geometry : angle 0.52979 (15030) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.43820 ( 2) hydrogen bonds : bond 0.04378 ( 606) hydrogen bonds : angle 4.12313 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.407 Fit side-chains REVERT: A 48 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7676 (ttp-110) REVERT: A 357 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 45 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 383 MET cc_start: 0.5484 (mtt) cc_final: 0.5062 (mmp) REVERT: B 422 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7039 (tm-30) REVERT: B 435 GLU cc_start: 0.4631 (OUTLIER) cc_final: 0.3982 (tp30) REVERT: C 149 ASN cc_start: 0.8545 (t0) cc_final: 0.8142 (t0) REVERT: C 164 GLN cc_start: 0.7573 (mt0) cc_final: 0.7145 (mp10) REVERT: C 187 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7665 (pttm) outliers start: 35 outliers final: 21 residues processed: 143 average time/residue: 0.6044 time to fit residues: 93.5198 Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105393 restraints weight = 12180.180| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.62 r_work: 0.3090 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11061 Z= 0.121 Angle : 0.518 8.600 15032 Z= 0.257 Chirality : 0.040 0.180 1802 Planarity : 0.004 0.049 1899 Dihedral : 8.524 85.275 1609 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 24.51 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.63 (0.22), residues: 1434 helix: 1.31 (0.17), residues: 880 sheet: 0.78 (0.63), residues: 75 loop : -1.33 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.011 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00281 (11060) covalent geometry : angle 0.51795 (15030) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.41691 ( 2) hydrogen bonds : bond 0.04003 ( 606) hydrogen bonds : angle 4.03262 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.475 Fit side-chains REVERT: A 48 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7708 (ttp-110) REVERT: A 57 MET cc_start: 0.7933 (ptt) cc_final: 0.7658 (pmm) REVERT: A 357 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 45 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6630 (mp) REVERT: B 383 MET cc_start: 0.5422 (mtt) cc_final: 0.4998 (mmp) REVERT: B 392 MET cc_start: 0.2987 (ppp) cc_final: 0.2059 (ppp) REVERT: B 422 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7050 (tm-30) REVERT: B 435 GLU cc_start: 0.4758 (OUTLIER) cc_final: 0.4080 (tp30) REVERT: C 32 TRP cc_start: 0.7950 (t60) cc_final: 0.7032 (t-100) REVERT: C 149 ASN cc_start: 0.8565 (t0) cc_final: 0.8131 (t0) REVERT: C 164 GLN cc_start: 0.7559 (mt0) cc_final: 0.7136 (mp10) REVERT: C 187 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7623 (pttm) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.5689 time to fit residues: 81.4935 Evaluate side-chains 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 48 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.185396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104632 restraints weight = 12217.115| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.62 r_work: 0.3078 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11061 Z= 0.124 Angle : 0.522 8.661 15032 Z= 0.259 Chirality : 0.040 0.181 1802 Planarity : 0.004 0.049 1899 Dihedral : 8.431 84.468 1609 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.12 % Allowed : 24.78 % Favored : 73.10 % 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: 0.63 (0.22), residues: 1434 helix: 1.32 (0.17), residues: 880 sheet: 0.65 (0.61), residues: 75 loop : -1.31 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.010 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00289 (11060) covalent geometry : angle 0.52172 (15030) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.35972 ( 2) hydrogen bonds : bond 0.04033 ( 606) hydrogen bonds : angle 4.02928 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.391 Fit side-chains REVERT: A 57 MET cc_start: 0.7950 (ptt) cc_final: 0.7669 (pmm) REVERT: A 357 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 45 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6656 (mp) REVERT: B 383 MET cc_start: 0.5342 (mtt) cc_final: 0.4937 (mmp) REVERT: B 392 MET cc_start: 0.2988 (ppp) cc_final: 0.2131 (ppp) REVERT: B 422 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7048 (tm-30) REVERT: B 435 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.4043 (tp30) REVERT: C 32 TRP cc_start: 0.7947 (t60) cc_final: 0.7051 (t-100) REVERT: C 149 ASN cc_start: 0.8558 (t0) cc_final: 0.8133 (t0) REVERT: C 164 GLN cc_start: 0.7553 (mt0) cc_final: 0.7162 (mp10) REVERT: C 187 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7601 (pttm) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.5828 time to fit residues: 84.7351 Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 118 optimal weight: 0.0070 chunk 89 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.186575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106818 restraints weight = 12181.781| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.56 r_work: 0.3110 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11061 Z= 0.109 Angle : 0.507 8.658 15032 Z= 0.252 Chirality : 0.039 0.178 1802 Planarity : 0.004 0.049 1899 Dihedral : 8.291 82.464 1609 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.04 % Allowed : 24.96 % Favored : 73.01 % 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: 0.72 (0.22), residues: 1434 helix: 1.41 (0.18), residues: 880 sheet: 0.52 (0.61), residues: 75 loop : -1.29 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 527 TRP 0.012 0.001 TRP B 245 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00250 (11060) covalent geometry : angle 0.50741 (15030) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.35949 ( 2) hydrogen bonds : bond 0.03754 ( 606) hydrogen bonds : angle 3.95465 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5992.08 seconds wall clock time: 102 minutes 19.39 seconds (6139.39 seconds total)