Starting phenix.real_space_refine on Fri Oct 23 18:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.cif Found real_map, /net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.map" model { file = "/net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25le_80182/10_2026/25le_80182.cif" } resolution = 3.22 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= 0.005 sd= 0.144 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 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6940 2.51 5 N 1690 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5259 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5259 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" 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: 2.68, per 1000 atoms: 0.25 Number of scatterers: 10586 At special positions: 0 Unit cell: (120.657, 95.656, 108.7, 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 2 19.00 S 60 16.00 P 4 15.00 O 1890 8.00 N 1690 7.00 C 6940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 314.9 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 6 sheets defined 62.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.745A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.546A pdb=" N GLY A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.995A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.070A pdb=" N VAL A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.856A pdb=" N MET A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 4.170A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.851A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.878A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.825A pdb=" N PHE A 242 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.654A pdb=" N LEU A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.943A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.540A pdb=" N ILE A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.704A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.599A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 438 removed outlier: 4.360A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 removed outlier: 3.879A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.895A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.975A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.724A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.686A pdb=" N GLU A 639 " --> pdb=" O PRO A 635 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.728A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 93 through 110 removed outlier: 3.550A pdb=" N GLY B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.994A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 removed outlier: 4.104A pdb=" N VAL B 153 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 4.094A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 199 removed outlier: 4.277A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.947A pdb=" N SER B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.912A pdb=" N VAL B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.827A pdb=" N PHE B 242 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.654A pdb=" N LEU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.941A pdb=" N VAL B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.574A pdb=" N LEU B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 302 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.705A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 368 through 402 removed outlier: 3.596A pdb=" N THR B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 removed outlier: 4.298A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 3.677A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 500 removed outlier: 3.898A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 537 removed outlier: 3.921A pdb=" N VAL B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 549 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 634 through 653 removed outlier: 3.794A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 removed outlier: 3.827A pdb=" N LYS B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.508A pdb=" N LYS B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.506A pdb=" N PHE B 757 " --> pdb=" O HIS B 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.147A pdb=" N ASN A 554 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.167A pdb=" N GLY A 560 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 591 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE A 562 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE A 593 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 730 through 739 removed outlier: 3.538A pdb=" N LEU A 777 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A 732 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 779 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 732 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 559 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU B 731 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU B 561 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLY B 733 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N TYR B 563 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR B 735 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 560 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 591 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE B 562 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 593 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA6, first strand: chain 'B' and resid 554 through 556 removed outlier: 5.879A pdb=" N ASN B 554 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 514 hydrogen bonds defined for protein. 1473 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: 1.86 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1607 1.31 - 1.44: 3024 1.44 - 1.56: 6079 1.56 - 1.68: 6 1.68 - 1.81: 104 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLY A 560 " pdb=" C GLY A 560 " ideal model delta sigma weight residual 1.520 1.467 0.053 7.30e-03 1.88e+04 5.36e+01 bond pdb=" CA SER A 744 " pdb=" CB SER A 744 " ideal model delta sigma weight residual 1.530 1.442 0.088 1.69e-02 3.50e+03 2.72e+01 bond pdb=" CA SER A 575 " pdb=" CB SER A 575 " ideal model delta sigma weight residual 1.534 1.455 0.078 1.58e-02 4.01e+03 2.46e+01 bond pdb=" CA PHE A 562 " pdb=" C PHE A 562 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.30e-02 5.92e+03 2.23e+01 bond pdb=" CA SER A 743 " pdb=" CB SER A 743 " ideal model delta sigma weight residual 1.531 1.459 0.072 1.52e-02 4.33e+03 2.22e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 13916 2.92 - 5.83: 651 5.83 - 8.75: 92 8.75 - 11.66: 32 11.66 - 14.58: 5 Bond angle restraints: 14696 Sorted by residual: angle pdb=" N PRO A 772 " pdb=" CA PRO A 772 " pdb=" CB PRO A 772 " ideal model delta sigma weight residual 103.32 93.71 9.61 8.40e-01 1.42e+00 1.31e+02 angle pdb=" N PRO A 635 " pdb=" CA PRO A 635 " pdb=" CB PRO A 635 " ideal model delta sigma weight residual 103.25 92.83 10.42 1.05e+00 9.07e-01 9.86e+01 angle pdb=" N LYS A 218 " pdb=" CA LYS A 218 " pdb=" C LYS A 218 " ideal model delta sigma weight residual 110.17 95.59 14.58 1.51e+00 4.39e-01 9.32e+01 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 113.02 98.72 14.30 1.49e+00 4.50e-01 9.21e+01 angle pdb=" N GLU A 537 " pdb=" CA GLU A 537 " pdb=" CB GLU A 537 " ideal model delta sigma weight residual 110.35 100.24 10.11 1.12e+00 7.97e-01 8.14e+01 ... (remaining 14691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 5544 19.09 - 38.19: 560 38.19 - 57.28: 191 57.28 - 76.37: 28 76.37 - 95.46: 9 Dihedral angle restraints: 6332 sinusoidal: 2456 harmonic: 3876 Sorted by residual: dihedral pdb=" CD ARG B 441 " pdb=" NE ARG B 441 " pdb=" CZ ARG B 441 " pdb=" NH1 ARG B 441 " ideal model delta sinusoidal sigma weight residual 0.00 -88.85 88.85 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CD ARG A 555 " pdb=" NE ARG A 555 " pdb=" CZ ARG A 555 " pdb=" NH1 ARG A 555 " ideal model delta sinusoidal sigma weight residual 0.00 85.82 -85.82 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CD ARG B 600 " pdb=" NE ARG B 600 " pdb=" CZ ARG B 600 " pdb=" NH1 ARG B 600 " ideal model delta sinusoidal sigma weight residual 0.00 52.58 -52.58 1 1.00e+01 1.00e-02 3.77e+01 ... (remaining 6329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1455 0.091 - 0.182: 204 0.182 - 0.273: 54 0.273 - 0.364: 12 0.364 - 0.455: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ILE B 217 " pdb=" N ILE B 217 " pdb=" C ILE B 217 " pdb=" CB ILE B 217 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA MET B 499 " pdb=" N MET B 499 " pdb=" C MET B 499 " pdb=" CB MET B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA GLU A 537 " pdb=" N GLU A 537 " pdb=" C GLU A 537 " pdb=" CB GLU A 537 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1723 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 441 " 1.124 9.50e-02 1.11e+02 5.04e-01 1.53e+02 pdb=" NE ARG B 441 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 441 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 441 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 441 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 555 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 555 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 555 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 555 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 555 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 606 " -0.871 9.50e-02 1.11e+02 3.90e-01 9.24e+01 pdb=" NE ARG A 606 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 606 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 606 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 606 " -0.024 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.71: 758 2.71 - 3.32: 11804 3.32 - 3.93: 19369 3.93 - 4.53: 28632 4.53 - 5.14: 45592 Nonbonded interactions: 106155 Sorted by model distance: nonbonded pdb=" OG1 THR B 735 " pdb=" O1A ADP B 901 " model vdw 2.107 3.040 nonbonded pdb=" O TYR B 289 " pdb=" OG1 THR B 293 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR A 735 " pdb=" O2A ADP A 901 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR A 79 " pdb=" O HOH A1001 " model vdw 2.189 3.040 nonbonded pdb=" O ILE B 208 " pdb=" OG SER B 212 " model vdw 2.191 3.040 ... (remaining 106150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.009 0.088 10820 Z= 0.536 Angle : 1.373 14.577 14696 Z= 0.902 Chirality : 0.075 0.455 1726 Planarity : 0.030 0.504 1782 Dihedral : 17.601 95.463 3852 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 1.98 % Allowed : 12.08 % Favored : 85.94 % Rotamer: Outliers : 9.88 % Allowed : 15.68 % Favored : 74.44 % Cbeta Deviations : 1.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.18), residues: 1316 helix: -3.19 (0.13), residues: 792 sheet: -2.02 (0.51), residues: 100 loop : -3.26 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 621 TYR 0.022 0.003 TYR A 289 PHE 0.019 0.002 PHE A 588 TRP 0.022 0.003 TRP B 370 HIS 0.009 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.54 (10820) covalent geometry : angle 1.37298 / 0.90 (14696) hydrogen bonds : bond 0.17679 / 11.25 ( 514) hydrogen bonds : angle 8.27169 / 5.72 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 182 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 142 MET cc_start: 0.7777 (mtp) cc_final: 0.7348 (mtm) REVERT: A 295 ARG cc_start: 0.7021 (ttp80) cc_final: 0.5263 (ttm110) REVERT: A 510 LEU cc_start: 0.8631 (mt) cc_final: 0.8379 (mt) REVERT: A 726 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8243 (mptt) REVERT: A 767 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (mmtm) REVERT: B 119 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7761 (mp) REVERT: B 631 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5279 (t0) REVERT: B 636 ASP cc_start: 0.6722 (t0) cc_final: 0.6463 (t0) outliers start: 114 outliers final: 75 residues processed: 275 average time/residue: 0.1105 time to fit residues: 41.4854 Evaluate side-chains 238 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 158 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 635 PRO Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 223 ASN A 273 HIS A 385 GLN A 419 GLN A 543 ASN A 546 GLN A 641 HIS B 179 ASN B 223 ASN B 273 HIS B 385 GLN B 543 ASN B 641 HIS B 716 GLN B 761 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.162305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.142749 restraints weight = 11887.476| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.92 r_work: 0.3407 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10820 Z= 0.154 Angle : 0.655 7.803 14696 Z= 0.342 Chirality : 0.043 0.157 1726 Planarity : 0.005 0.077 1782 Dihedral : 10.758 94.681 1637 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.52 % Favored : 92.33 % Rotamer: Outliers : 5.46 % Allowed : 18.98 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.22), residues: 1316 helix: -1.67 (0.17), residues: 814 sheet: -1.97 (0.49), residues: 108 loop : -2.31 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 295 TYR 0.017 0.002 TYR A 755 PHE 0.012 0.001 PHE B 440 TRP 0.012 0.002 TRP B 258 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10820) covalent geometry : angle 0.65487 / 0.34 (14696) hydrogen bonds : bond 0.04676 / 3.10 ( 514) hydrogen bonds : angle 4.92177 / 3.47 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 142 MET cc_start: 0.8200 (mtp) cc_final: 0.7831 (mtm) REVERT: A 158 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.4767 (m-80) REVERT: A 474 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4835 (tppt) REVERT: A 510 LEU cc_start: 0.8525 (mt) cc_final: 0.8285 (mt) REVERT: A 600 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.5879 (ptp-170) REVERT: A 615 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7441 (ttmm) REVERT: B 119 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 142 MET cc_start: 0.8699 (mmm) cc_final: 0.8429 (mmm) REVERT: B 158 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: B 218 LYS cc_start: 0.6815 (mttt) cc_final: 0.6600 (ttpp) REVERT: B 295 ARG cc_start: 0.6797 (ttp80) cc_final: 0.5067 (ttm-80) REVERT: B 499 MET cc_start: 0.7671 (tpt) cc_final: 0.6124 (ptt) outliers start: 63 outliers final: 35 residues processed: 218 average time/residue: 0.0977 time to fit residues: 30.0385 Evaluate side-chains 190 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [36, 54, 66, 117, 75, 71, 37, 65, 57, 106, 52] chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.166340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.146336 restraints weight = 11785.940| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.97 r_work: 0.3455 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10820 Z= 0.108 Angle : 0.573 7.927 14696 Z= 0.295 Chirality : 0.041 0.133 1726 Planarity : 0.004 0.055 1782 Dihedral : 8.427 101.589 1520 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 4.33 % Allowed : 21.14 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.24), residues: 1316 helix: -0.73 (0.19), residues: 810 sheet: -1.73 (0.49), residues: 108 loop : -1.76 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.018 0.001 TYR A 500 PHE 0.015 0.001 PHE B 642 TRP 0.011 0.001 TRP A 258 HIS 0.003 0.000 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10820) covalent geometry : angle 0.57309 / 0.29 (14696) hydrogen bonds : bond 0.03510 / 2.35 ( 514) hydrogen bonds : angle 4.32495 / 3.07 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 142 MET cc_start: 0.8126 (mtp) cc_final: 0.7732 (mtm) REVERT: A 151 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: A 314 MET cc_start: 0.8058 (mtp) cc_final: 0.7530 (ttm) REVERT: A 328 ILE cc_start: 0.8338 (mt) cc_final: 0.7782 (tt) REVERT: A 387 MET cc_start: 0.8186 (mmp) cc_final: 0.7937 (mmp) REVERT: A 441 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7222 (ptm-80) REVERT: A 474 LYS cc_start: 0.5324 (OUTLIER) cc_final: 0.4668 (tppt) REVERT: A 491 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: B 119 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 136 ILE cc_start: 0.7860 (mm) cc_final: 0.7640 (mt) REVERT: B 142 MET cc_start: 0.8678 (mmm) cc_final: 0.8408 (mmm) REVERT: B 211 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7886 (mt) REVERT: B 328 ILE cc_start: 0.8343 (mt) cc_final: 0.7730 (pt) REVERT: B 387 MET cc_start: 0.8088 (mmp) cc_final: 0.7764 (mmp) REVERT: B 499 MET cc_start: 0.7658 (tpt) cc_final: 0.5917 (ptt) outliers start: 50 outliers final: 25 residues processed: 210 average time/residue: 0.1001 time to fit residues: 29.9024 Evaluate side-chains 183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [78, 22, 99, 45, 5, 62, 104, 86, 80, 72, 53] chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 80 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 419 GLN A 448 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.165633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.144948 restraints weight = 11935.329| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.03 r_work: 0.3424 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10820 Z= 0.118 Angle : 0.578 6.428 14696 Z= 0.294 Chirality : 0.041 0.150 1726 Planarity : 0.004 0.050 1782 Dihedral : 7.813 105.232 1498 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.37 % Allowed : 21.49 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.24), residues: 1316 helix: -0.41 (0.19), residues: 814 sheet: -1.59 (0.51), residues: 106 loop : -1.60 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.018 0.001 TYR A 500 PHE 0.009 0.001 PHE B 440 TRP 0.010 0.001 TRP A 258 HIS 0.002 0.000 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10820) covalent geometry : angle 0.57828 / 0.29 (14696) hydrogen bonds : bond 0.03672 / 2.44 ( 514) hydrogen bonds : angle 4.21728 / 2.99 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 119 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7451 (mp) REVERT: A 136 ILE cc_start: 0.7889 (mm) cc_final: 0.7663 (mt) REVERT: A 142 MET cc_start: 0.8207 (mtp) cc_final: 0.7857 (mtm) REVERT: A 151 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5890 (pm20) REVERT: A 158 TYR cc_start: 0.6189 (OUTLIER) cc_final: 0.4473 (m-80) REVERT: A 218 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6566 (mttp) REVERT: A 314 MET cc_start: 0.8240 (mtp) cc_final: 0.7721 (ttm) REVERT: A 328 ILE cc_start: 0.8443 (mt) cc_final: 0.7889 (tt) REVERT: A 441 ARG cc_start: 0.7462 (ptm160) cc_final: 0.7259 (ptm-80) REVERT: A 491 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 605 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: B 112 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 119 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7464 (mp) REVERT: B 136 ILE cc_start: 0.7933 (mm) cc_final: 0.7724 (mt) REVERT: B 158 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: B 211 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (mt) REVERT: B 328 ILE cc_start: 0.8440 (mt) cc_final: 0.7891 (tt) REVERT: B 499 MET cc_start: 0.7735 (tpt) cc_final: 0.5971 (ptt) REVERT: B 593 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (mm) REVERT: B 619 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7588 (mtp) outliers start: 62 outliers final: 37 residues processed: 205 average time/residue: 0.0950 time to fit residues: 28.1806 Evaluate side-chains 196 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [100, 87, 114, 78, 14, 85, 44, 66, 31, 19, 59] chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.165102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146656 restraints weight = 11771.078| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.00 r_work: 0.3417 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10820 Z= 0.122 Angle : 0.571 6.768 14696 Z= 0.291 Chirality : 0.041 0.141 1726 Planarity : 0.004 0.051 1782 Dihedral : 7.467 107.129 1490 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.37 % Allowed : 21.66 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.24), residues: 1316 helix: -0.32 (0.19), residues: 820 sheet: -1.41 (0.51), residues: 106 loop : -1.50 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 606 TYR 0.017 0.001 TYR B 500 PHE 0.007 0.001 PHE B 440 TRP 0.011 0.001 TRP A 258 HIS 0.001 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10820) covalent geometry : angle 0.57144 / 0.29 (14696) hydrogen bonds : bond 0.03720 / 2.49 ( 514) hydrogen bonds : angle 4.17164 / 2.96 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8493 (t0) cc_final: 0.8217 (t0) REVERT: A 112 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 119 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 136 ILE cc_start: 0.7904 (mm) cc_final: 0.7680 (mt) REVERT: A 142 MET cc_start: 0.8183 (mtp) cc_final: 0.7860 (mtm) REVERT: A 151 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5785 (pm20) REVERT: A 158 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: A 218 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6496 (mttp) REVERT: A 314 MET cc_start: 0.8365 (mtp) cc_final: 0.7765 (ttm) REVERT: A 328 ILE cc_start: 0.8465 (mt) cc_final: 0.7934 (tt) REVERT: A 441 ARG cc_start: 0.7464 (ptm160) cc_final: 0.7243 (ptm-80) REVERT: A 464 MET cc_start: 0.7777 (mmm) cc_final: 0.7352 (mtp) REVERT: A 491 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 605 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6141 (mt-10) REVERT: B 112 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 119 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7495 (mp) REVERT: B 136 ILE cc_start: 0.7929 (mm) cc_final: 0.7728 (mt) REVERT: B 158 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.4656 (m-80) REVERT: B 211 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 328 ILE cc_start: 0.8478 (mt) cc_final: 0.7908 (tt) REVERT: B 464 MET cc_start: 0.7783 (mmm) cc_final: 0.7380 (mtp) REVERT: B 491 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: B 499 MET cc_start: 0.7731 (tpt) cc_final: 0.5938 (ptt) REVERT: B 619 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7646 (mtp) outliers start: 62 outliers final: 39 residues processed: 206 average time/residue: 0.0949 time to fit residues: 28.6736 Evaluate side-chains 198 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [65, 4, 97, 112, 90, 60, 78, 111, 80, 95, 25] chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 97 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 0.0370 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.150738 restraints weight = 11833.641| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 0.97 r_work: 0.3491 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.002 0.027 10820 Z= 0.092 Angle : 0.533 6.984 14696 Z= 0.271 Chirality : 0.040 0.132 1726 Planarity : 0.004 0.050 1782 Dihedral : 7.140 108.251 1488 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.99 % Allowed : 22.88 % Favored : 73.14 % 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: -0.76 (0.25), residues: 1316 helix: 0.10 (0.20), residues: 814 sheet: -1.25 (0.52), residues: 106 loop : -1.33 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.016 0.001 TYR A 500 PHE 0.009 0.001 PHE B 642 TRP 0.010 0.001 TRP A 258 HIS 0.001 0.000 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (10820) covalent geometry : angle 0.53323 / 0.27 (14696) hydrogen bonds : bond 0.03047 / 2.05 ( 514) hydrogen bonds : angle 3.97002 / 2.83 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 119 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7334 (mp) REVERT: A 136 ILE cc_start: 0.7757 (mm) cc_final: 0.7550 (mt) REVERT: A 142 MET cc_start: 0.7943 (mtp) cc_final: 0.7566 (mtm) REVERT: A 151 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5702 (pm20) REVERT: A 158 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.4113 (m-80) REVERT: A 218 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6104 (mttp) REVERT: A 328 ILE cc_start: 0.8321 (mt) cc_final: 0.7776 (tt) REVERT: A 464 MET cc_start: 0.7585 (mmm) cc_final: 0.7135 (mtp) REVERT: A 491 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 605 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5708 (mt-10) REVERT: B 112 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8201 (tt) REVERT: B 119 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7354 (mp) REVERT: B 142 MET cc_start: 0.8569 (mmm) cc_final: 0.8284 (mmm) REVERT: B 211 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8092 (mt) REVERT: B 232 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5728 (tp) REVERT: B 328 ILE cc_start: 0.8352 (mt) cc_final: 0.7748 (pt) REVERT: B 464 MET cc_start: 0.7555 (mmm) cc_final: 0.7114 (mtp) REVERT: B 491 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: B 499 MET cc_start: 0.7472 (tpt) cc_final: 0.5791 (ptt) outliers start: 46 outliers final: 25 residues processed: 202 average time/residue: 0.0909 time to fit residues: 26.7131 Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [5, 123, 49, 126, 32, 62, 96, 84, 124, 50, 13] chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 90 ASN B 448 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.164938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.146414 restraints weight = 11782.531| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.98 r_work: 0.3416 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10820 Z= 0.148 Angle : 0.600 7.436 14696 Z= 0.304 Chirality : 0.043 0.149 1726 Planarity : 0.004 0.046 1782 Dihedral : 7.251 108.795 1486 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.25 % Allowed : 23.40 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 1316 helix: -0.15 (0.19), residues: 824 sheet: -1.16 (0.51), residues: 106 loop : -1.34 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.018 0.002 TYR B 500 PHE 0.010 0.001 PHE B 440 TRP 0.011 0.002 TRP B 258 HIS 0.002 0.000 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10820) covalent geometry : angle 0.60034 / 0.30 (14696) hydrogen bonds : bond 0.03990 / 2.68 ( 514) hydrogen bonds : angle 4.17384 / 2.95 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8502 (t0) cc_final: 0.8259 (t0) REVERT: A 112 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 119 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7432 (mp) REVERT: A 136 ILE cc_start: 0.7856 (mm) cc_final: 0.7635 (mt) REVERT: A 151 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: A 158 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4218 (m-10) REVERT: A 218 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6318 (mttp) REVERT: A 328 ILE cc_start: 0.8417 (mt) cc_final: 0.7874 (tt) REVERT: A 464 MET cc_start: 0.7730 (mmm) cc_final: 0.7326 (mtp) REVERT: A 605 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.6033 (mt-10) REVERT: A 722 LYS cc_start: 0.7896 (tttm) cc_final: 0.7626 (tttp) REVERT: B 112 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8172 (tt) REVERT: B 119 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7432 (mp) REVERT: B 211 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8040 (mt) REVERT: B 328 ILE cc_start: 0.8420 (mt) cc_final: 0.7886 (tt) REVERT: B 464 MET cc_start: 0.7762 (mmm) cc_final: 0.7350 (mtp) REVERT: B 499 MET cc_start: 0.7678 (tpt) cc_final: 0.5853 (ptt) REVERT: B 619 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7521 (mtp) outliers start: 49 outliers final: 31 residues processed: 184 average time/residue: 0.0990 time to fit residues: 26.1643 Evaluate side-chains 178 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [95, 112, 55, 82, 24, 16, 53, 1, 103, 4, 96] chunk 95 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 103 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.167551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148930 restraints weight = 11820.484| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.02 r_work: 0.3431 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10820 Z= 0.114 Angle : 0.565 7.532 14696 Z= 0.287 Chirality : 0.041 0.150 1726 Planarity : 0.004 0.051 1782 Dihedral : 7.162 108.572 1486 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.99 % Allowed : 23.48 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1316 helix: 0.07 (0.19), residues: 816 sheet: -1.11 (0.52), residues: 106 loop : -1.41 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.012 0.001 TYR B 289 PHE 0.007 0.001 PHE A 487 TRP 0.011 0.001 TRP A 258 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10820) covalent geometry : angle 0.56519 / 0.29 (14696) hydrogen bonds : bond 0.03563 / 2.38 ( 514) hydrogen bonds : angle 4.07184 / 2.89 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8499 (t0) cc_final: 0.8240 (t0) REVERT: A 112 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 119 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 151 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: A 158 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4075 (m-80) REVERT: A 218 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6218 (mttp) REVERT: A 328 ILE cc_start: 0.8385 (mt) cc_final: 0.7841 (tt) REVERT: A 464 MET cc_start: 0.7656 (mmm) cc_final: 0.7238 (mtp) REVERT: A 605 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5887 (mt-10) REVERT: A 722 LYS cc_start: 0.7869 (tttm) cc_final: 0.7597 (tttp) REVERT: B 112 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 119 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 211 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 328 ILE cc_start: 0.8406 (mt) cc_final: 0.7837 (tt) REVERT: B 464 MET cc_start: 0.7754 (mmm) cc_final: 0.7366 (mtp) REVERT: B 499 MET cc_start: 0.7675 (tpt) cc_final: 0.5859 (ptt) outliers start: 46 outliers final: 31 residues processed: 181 average time/residue: 0.0933 time to fit residues: 24.7151 Evaluate side-chains 176 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [123, 38, 131, 126, 67, 32, 117, 55, 96, 107, 92] chunk 123 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.166759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147878 restraints weight = 11838.899| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 0.88 r_work: 0.3458 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10820 Z= 0.115 Angle : 0.567 7.703 14696 Z= 0.287 Chirality : 0.041 0.150 1726 Planarity : 0.004 0.049 1782 Dihedral : 7.093 107.656 1486 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.99 % Allowed : 23.48 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1316 helix: 0.06 (0.19), residues: 830 sheet: -1.07 (0.52), residues: 106 loop : -1.38 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 606 TYR 0.020 0.001 TYR B 500 PHE 0.007 0.001 PHE B 487 TRP 0.011 0.001 TRP B 258 HIS 0.001 0.000 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10820) covalent geometry : angle 0.56703 / 0.29 (14696) hydrogen bonds : bond 0.03565 / 2.39 ( 514) hydrogen bonds : angle 4.08352 / 2.90 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8480 (t0) cc_final: 0.8223 (t0) REVERT: A 112 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 119 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 151 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: A 158 TYR cc_start: 0.6028 (OUTLIER) cc_final: 0.4095 (m-80) REVERT: A 218 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6288 (mttp) REVERT: A 328 ILE cc_start: 0.8391 (mt) cc_final: 0.7858 (tt) REVERT: A 464 MET cc_start: 0.7643 (mmm) cc_final: 0.7209 (mtp) REVERT: A 722 LYS cc_start: 0.7767 (tttm) cc_final: 0.7494 (tttp) REVERT: B 112 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8183 (tt) REVERT: B 119 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 211 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 328 ILE cc_start: 0.8407 (mt) cc_final: 0.7842 (tt) REVERT: B 464 MET cc_start: 0.7720 (mmm) cc_final: 0.7317 (mtp) REVERT: B 499 MET cc_start: 0.7619 (tpt) cc_final: 0.5836 (ptt) REVERT: B 619 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7472 (mtp) outliers start: 46 outliers final: 32 residues processed: 179 average time/residue: 0.0964 time to fit residues: 24.9979 Evaluate side-chains 182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [81, 13, 11, 7, 33, 83, 10, 16, 59, 30, 119] chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 0.0370 chunk 119 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.169045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.150956 restraints weight = 11844.236| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.01 r_work: 0.3462 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10820 Z= 0.099 Angle : 0.547 7.796 14696 Z= 0.277 Chirality : 0.041 0.142 1726 Planarity : 0.004 0.051 1782 Dihedral : 6.977 106.510 1486 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.55 % Allowed : 23.83 % Favored : 72.62 % 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: -0.57 (0.25), residues: 1316 helix: 0.24 (0.19), residues: 828 sheet: -1.01 (0.52), residues: 106 loop : -1.34 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 441 TYR 0.013 0.001 TYR A 500 PHE 0.007 0.001 PHE A 487 TRP 0.011 0.001 TRP B 258 HIS 0.001 0.000 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (10820) covalent geometry : angle 0.54723 / 0.28 (14696) hydrogen bonds : bond 0.03229 / 2.17 ( 514) hydrogen bonds : angle 3.96797 / 2.82 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 119 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 151 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: A 218 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6025 (mttm) REVERT: A 328 ILE cc_start: 0.8379 (mt) cc_final: 0.7795 (tt) REVERT: A 441 ARG cc_start: 0.7333 (ptm-80) cc_final: 0.7048 (ptp-170) REVERT: A 464 MET cc_start: 0.7613 (mmm) cc_final: 0.7152 (mtp) REVERT: A 722 LYS cc_start: 0.7694 (tttm) cc_final: 0.7446 (tttp) REVERT: B 112 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (tt) REVERT: B 119 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 211 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 232 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5726 (tp) REVERT: B 328 ILE cc_start: 0.8393 (mt) cc_final: 0.7834 (tt) REVERT: B 464 MET cc_start: 0.7665 (mmm) cc_final: 0.7232 (mtp) REVERT: B 499 MET cc_start: 0.7531 (tpt) cc_final: 0.5815 (ptt) outliers start: 41 outliers final: 30 residues processed: 181 average time/residue: 0.1013 time to fit residues: 26.5609 Evaluate side-chains 181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 717 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [48, 45, 128, 43, 87, 80, 105, 25, 118, 36, 68] chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.166387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148076 restraints weight = 11825.231| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.00 r_work: 0.3430 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10820 Z= 0.129 Angle : 0.580 7.839 14696 Z= 0.294 Chirality : 0.042 0.154 1726 Planarity : 0.004 0.049 1782 Dihedral : 7.042 106.651 1486 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.29 % Allowed : 24.00 % Favored : 72.70 % 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: -0.64 (0.24), residues: 1316 helix: 0.13 (0.19), residues: 828 sheet: -1.01 (0.52), residues: 106 loop : -1.23 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 400 TYR 0.019 0.001 TYR B 500 PHE 0.008 0.001 PHE A 487 TRP 0.011 0.001 TRP B 258 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10820) covalent geometry : angle 0.57979 / 0.29 (14696) hydrogen bonds : bond 0.03720 / 2.49 ( 514) hydrogen bonds : angle 4.09959 / 2.91 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.80 seconds wall clock time: 46 minutes 41.63 seconds (2801.63 seconds total)