Starting phenix.real_space_refine on Thu Feb 5 00:30:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.map" model { file = "/net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byb_45025/02_2026/9byb_45025.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 84 5.16 5 C 8802 2.51 5 N 2190 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 6779 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 32, 'TRANS': 849} Chain: "B" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 6779 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 32, 'TRANS': 849} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' MG': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' MG': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Time building chain proxies: 3.29, per 1000 atoms: 0.24 Number of scatterers: 13664 At special positions: 0 Unit cell: (107.168, 92.984, 227.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 4 15.00 Mg 2 11.99 O 2582 8.00 N 2190 7.00 C 8802 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: 1.40 Conformation dependent library (CDL) restraints added in 635.6 milliseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 53.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.182A pdb=" N GLN A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 103 removed outlier: 3.596A pdb=" N ILE A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.644A pdb=" N GLU A 109 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 removed outlier: 4.476A pdb=" N ILE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 267 through 298 removed outlier: 3.507A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.510A pdb=" N LEU A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.577A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 384 through 397 removed outlier: 3.664A pdb=" N LEU A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 467 through 475 removed outlier: 4.167A pdb=" N MET A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 505 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.772A pdb=" N SER A 530 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.557A pdb=" N LYS A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 596 Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.620A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.603A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 675 through 707 removed outlier: 4.212A pdb=" N GLU A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 759 through 765 removed outlier: 3.508A pdb=" N PHE A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 4.034A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 818 through 827 removed outlier: 3.703A pdb=" N GLN A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 846 through 858 removed outlier: 3.699A pdb=" N PHE A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 879 through 904 removed outlier: 4.253A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 894 " --> pdb=" O MET A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.950A pdb=" N ARG B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 101 removed outlier: 4.129A pdb=" N ILE B 89 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 114 through 139 removed outlier: 3.870A pdb=" N GLU B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 267 through 298 removed outlier: 3.580A pdb=" N VAL B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.748A pdb=" N THR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 337 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 384 through 397 Processing helix chain 'B' and resid 403 through 416 Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 488 through 504 Processing helix chain 'B' and resid 526 through 530 removed outlier: 3.648A pdb=" N SER B 530 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.540A pdb=" N ILE B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 607 removed outlier: 3.642A pdb=" N ALA B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 629 Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 659 through 666 Processing helix chain 'B' and resid 676 through 709 removed outlier: 3.685A pdb=" N LYS B 680 " --> pdb=" O MET B 676 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 702 " --> pdb=" O MET B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 734 Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.896A pdb=" N VAL B 762 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 787 removed outlier: 3.698A pdb=" N SER B 774 " --> pdb=" O GLY B 770 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B 776 " --> pdb=" O THR B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.760A pdb=" N THR B 792 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 827 Processing helix chain 'B' and resid 828 through 833 Processing helix chain 'B' and resid 846 through 861 removed outlier: 3.659A pdb=" N GLY B 858 " --> pdb=" O MET B 854 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 859 " --> pdb=" O GLY B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 906 removed outlier: 4.190A pdb=" N TRP B 883 " --> pdb=" O ASN B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 155 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 176 removed outlier: 6.084A pdb=" N VAL A 243 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 245 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 186 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.001A pdb=" N LEU A 194 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 234 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 removed outlier: 7.364A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 378 removed outlier: 6.621A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP A 378 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N MET A 535 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 534 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN A 514 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 536 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 446 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 435 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 378 removed outlier: 6.621A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP A 378 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N MET A 535 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 536 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176 removed outlier: 6.339A pdb=" N TYR B 241 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 194 through 197 removed outlier: 4.205A pdb=" N LEU B 194 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 564 removed outlier: 7.308A pdb=" N VAL B 633 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 653 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR B 635 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 375 removed outlier: 7.031A pdb=" N ALA B 539 " --> pdb=" O MET B 374 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 432 through 439 removed outlier: 5.661A pdb=" N LYS B 432 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS B 450 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B 438 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG B 444 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS B 459 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR B 453 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N THR B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL B 512 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU B 477 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLY B 536 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N GLU B 479 " --> pdb=" O GLY B 536 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1968 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: 1.76 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2359 1.32 - 1.45: 3305 1.45 - 1.57: 8070 1.57 - 1.70: 8 1.70 - 1.82: 156 Bond restraints: 13898 Sorted by residual: bond pdb=" CA THR A 780 " pdb=" C THR A 780 " ideal model delta sigma weight residual 1.522 1.493 0.030 1.38e-02 5.25e+03 4.57e+00 bond pdb=" C PHE A 765 " pdb=" N MET A 766 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.50e-02 4.44e+03 4.55e+00 bond pdb=" CA MET B 146 " pdb=" CB MET B 146 " ideal model delta sigma weight residual 1.518 1.554 -0.036 2.08e-02 2.31e+03 3.00e+00 bond pdb=" CA GLY A 816 " pdb=" C GLY A 816 " ideal model delta sigma weight residual 1.515 1.504 0.010 6.20e-03 2.60e+04 2.83e+00 bond pdb=" N LEU B 909 " pdb=" CA LEU B 909 " ideal model delta sigma weight residual 1.453 1.474 -0.021 1.31e-02 5.83e+03 2.61e+00 ... (remaining 13893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 18614 3.16 - 6.33: 172 6.33 - 9.49: 25 9.49 - 12.65: 10 12.65 - 15.81: 1 Bond angle restraints: 18822 Sorted by residual: angle pdb=" N GLY A 816 " pdb=" CA GLY A 816 " pdb=" C GLY A 816 " ideal model delta sigma weight residual 110.21 104.67 5.54 9.10e-01 1.21e+00 3.71e+01 angle pdb=" N ILE A 769 " pdb=" CA ILE A 769 " pdb=" C ILE A 769 " ideal model delta sigma weight residual 112.90 107.41 5.49 9.60e-01 1.09e+00 3.27e+01 angle pdb=" CA LYS B 145 " pdb=" CB LYS B 145 " pdb=" CG LYS B 145 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 angle pdb=" CB MET B 146 " pdb=" CG MET B 146 " pdb=" SD MET B 146 " ideal model delta sigma weight residual 112.70 128.51 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N ILE A 850 " pdb=" CA ILE A 850 " pdb=" C ILE A 850 " ideal model delta sigma weight residual 111.81 107.58 4.23 8.60e-01 1.35e+00 2.42e+01 ... (remaining 18817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7196 17.94 - 35.88: 930 35.88 - 53.83: 272 53.83 - 71.77: 31 71.77 - 89.71: 19 Dihedral angle restraints: 8448 sinusoidal: 3346 harmonic: 5102 Sorted by residual: dihedral pdb=" CA TRP A 817 " pdb=" C TRP A 817 " pdb=" N PHE A 818 " pdb=" CA PHE A 818 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU B 908 " pdb=" C GLU B 908 " pdb=" N LEU B 909 " pdb=" CA LEU B 909 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA VAL B 746 " pdb=" C VAL B 746 " pdb=" N ASP B 747 " pdb=" CA ASP B 747 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 8445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1439 0.038 - 0.076: 590 0.076 - 0.114: 187 0.114 - 0.152: 44 0.152 - 0.189: 8 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA ILE A 837 " pdb=" N ILE A 837 " pdb=" C ILE A 837 " pdb=" CB ILE A 837 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA MET B 146 " pdb=" N MET B 146 " pdb=" C MET B 146 " pdb=" CB MET B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CG LEU A 93 " pdb=" CB LEU A 93 " pdb=" CD1 LEU A 93 " pdb=" CD2 LEU A 93 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 2265 not shown) Planarity restraints: 2338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 908 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C GLU B 908 " 0.077 2.00e-02 2.50e+03 pdb=" O GLU B 908 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU B 909 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 908 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C GLU A 908 " -0.071 2.00e-02 2.50e+03 pdb=" O GLU A 908 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 909 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 343 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ILE B 343 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE B 343 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 344 " 0.017 2.00e-02 2.50e+03 ... (remaining 2335 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 69 2.44 - 3.06: 9465 3.06 - 3.67: 21761 3.67 - 4.29: 30505 4.29 - 4.90: 50378 Nonbonded interactions: 112178 Sorted by model distance: nonbonded pdb=" OD1 ASN A 706 " pdb="MG MG A1001 " model vdw 1.828 2.170 nonbonded pdb=" OD1 ASN B 706 " pdb="MG MG B1001 " model vdw 1.940 2.170 nonbonded pdb=" O SER B 354 " pdb=" OG SER B 632 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR A 397 " pdb=" O SER A 427 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" O THR A 247 " model vdw 2.196 3.040 ... (remaining 112173 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.004 0.048 13898 Z= 0.197 Angle : 0.841 15.814 18822 Z= 0.452 Chirality : 0.046 0.189 2268 Planarity : 0.005 0.060 2338 Dihedral : 17.481 89.711 5144 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.75 % Favored : 90.51 % Rotamer: Outliers : 4.09 % Allowed : 28.17 % Favored : 67.74 % Cbeta Deviations : 0.06 % 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: -1.70 (0.20), residues: 1760 helix: -0.41 (0.17), residues: 880 sheet: 0.12 (0.47), residues: 136 loop : -2.25 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 492 TYR 0.049 0.002 TYR B 430 PHE 0.020 0.002 PHE B 776 TRP 0.012 0.001 TRP B 883 HIS 0.012 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00426 (13898) covalent geometry : angle 0.84056 (18822) hydrogen bonds : bond 0.17106 ( 692) hydrogen bonds : angle 7.10360 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: A 231 MET cc_start: 0.8244 (mtp) cc_final: 0.8012 (mtp) REVERT: A 377 LEU cc_start: 0.8781 (tp) cc_final: 0.8342 (tp) REVERT: A 392 PHE cc_start: 0.8476 (t80) cc_final: 0.8062 (t80) REVERT: A 407 LEU cc_start: 0.9577 (tp) cc_final: 0.9341 (mm) REVERT: A 776 PHE cc_start: 0.8691 (m-80) cc_final: 0.8421 (m-80) REVERT: A 854 MET cc_start: 0.8529 (mmm) cc_final: 0.8256 (mmm) REVERT: A 879 ASN cc_start: 0.8695 (t0) cc_final: 0.8477 (t0) REVERT: A 890 MET cc_start: 0.8783 (ttp) cc_final: 0.8390 (ttp) REVERT: B 91 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 111 ASN cc_start: 0.5658 (OUTLIER) cc_final: 0.5151 (t160) REVERT: B 462 MET cc_start: 0.5401 (pmm) cc_final: 0.5080 (ppp) REVERT: B 471 MET cc_start: -0.2493 (mmt) cc_final: -0.3033 (tpp) REVERT: B 504 GLU cc_start: 0.9082 (pp20) cc_final: 0.8867 (pp20) REVERT: B 532 MET cc_start: 0.6266 (ttp) cc_final: 0.5875 (ttm) REVERT: B 535 MET cc_start: 0.5380 (mtt) cc_final: 0.2377 (ptm) REVERT: B 546 GLU cc_start: 0.8582 (pm20) cc_final: 0.7627 (tm-30) REVERT: B 733 ILE cc_start: 0.9022 (tp) cc_final: 0.8728 (mt) outliers start: 62 outliers final: 50 residues processed: 214 average time/residue: 0.0917 time to fit residues: 31.9248 Evaluate side-chains 212 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 895 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 347 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 347 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.155535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100432 restraints weight = 27613.830| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.70 r_work: 0.3385 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13898 Z= 0.331 Angle : 0.826 12.519 18822 Z= 0.419 Chirality : 0.050 0.378 2268 Planarity : 0.006 0.057 2338 Dihedral : 9.549 70.082 2025 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.92 % Favored : 90.28 % Rotamer: Outliers : 6.60 % Allowed : 24.93 % Favored : 68.47 % 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: -1.56 (0.20), residues: 1760 helix: -0.26 (0.17), residues: 896 sheet: 0.10 (0.46), residues: 134 loop : -2.24 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 492 TYR 0.033 0.002 TYR A 494 PHE 0.025 0.002 PHE B 776 TRP 0.010 0.002 TRP B 817 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd covalent geometry : bond 0.00782 (13898) covalent geometry : angle 0.82559 (18822) hydrogen bonds : bond 0.04719 ( 692) hydrogen bonds : angle 5.38603 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 161 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: A 141 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 231 MET cc_start: 0.8345 (mtp) cc_final: 0.8096 (mtp) REVERT: A 316 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 377 LEU cc_start: 0.8816 (tp) cc_final: 0.8255 (tp) REVERT: A 392 PHE cc_start: 0.8392 (t80) cc_final: 0.8120 (t80) REVERT: A 397 TYR cc_start: 0.8070 (m-80) cc_final: 0.7845 (m-10) REVERT: A 407 LEU cc_start: 0.9582 (tp) cc_final: 0.9340 (mm) REVERT: A 571 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8791 (mmmm) REVERT: A 656 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: A 806 TYR cc_start: 0.7757 (t80) cc_final: 0.7162 (t80) REVERT: A 854 MET cc_start: 0.8612 (mmm) cc_final: 0.8322 (mmm) REVERT: A 856 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 91 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: B 373 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 405 MET cc_start: 0.9327 (mpp) cc_final: 0.9098 (mpp) REVERT: B 430 TYR cc_start: 0.6901 (t80) cc_final: 0.6564 (t80) REVERT: B 535 MET cc_start: 0.5283 (mtt) cc_final: 0.2279 (ptm) REVERT: B 542 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8513 (p0) REVERT: B 546 GLU cc_start: 0.8568 (pm20) cc_final: 0.7787 (tm-30) REVERT: B 693 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9139 (tp) outliers start: 100 outliers final: 59 residues processed: 243 average time/residue: 0.0875 time to fit residues: 34.1328 Evaluate side-chains 223 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 154 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 895 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 814 HIS B 84 ASN B 111 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.148408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092708 restraints weight = 27366.888| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.70 r_work: 0.3441 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13898 Z= 0.212 Angle : 0.725 12.455 18822 Z= 0.366 Chirality : 0.046 0.356 2268 Planarity : 0.005 0.059 2338 Dihedral : 8.772 62.361 1984 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.35 % Favored : 90.91 % Rotamer: Outliers : 6.73 % Allowed : 25.13 % Favored : 68.14 % 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: -1.37 (0.20), residues: 1760 helix: -0.07 (0.17), residues: 908 sheet: 0.07 (0.45), residues: 139 loop : -2.22 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.014 0.002 TYR B 806 PHE 0.023 0.002 PHE B 440 TRP 0.009 0.001 TRP B 817 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00497 (13898) covalent geometry : angle 0.72455 (18822) hydrogen bonds : bond 0.04146 ( 692) hydrogen bonds : angle 5.05366 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 163 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: A 231 MET cc_start: 0.8420 (mtp) cc_final: 0.8194 (mtp) REVERT: A 316 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 377 LEU cc_start: 0.8867 (tp) cc_final: 0.8341 (tp) REVERT: A 392 PHE cc_start: 0.8237 (t80) cc_final: 0.7915 (t80) REVERT: A 407 LEU cc_start: 0.9484 (tp) cc_final: 0.9283 (mm) REVERT: A 571 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8764 (mmmm) REVERT: A 638 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8223 (p0) REVERT: A 806 TYR cc_start: 0.7533 (t80) cc_final: 0.7031 (t80) REVERT: A 854 MET cc_start: 0.8552 (mmm) cc_final: 0.8279 (mmm) REVERT: A 856 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7632 (mp) REVERT: A 879 ASN cc_start: 0.8738 (t0) cc_final: 0.8468 (t0) REVERT: B 91 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: B 111 ASN cc_start: 0.5651 (OUTLIER) cc_final: 0.5051 (t160) REVERT: B 373 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7678 (mm) REVERT: B 430 TYR cc_start: 0.7130 (t80) cc_final: 0.6819 (t80) REVERT: B 542 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8666 (p0) REVERT: B 546 GLU cc_start: 0.8332 (pm20) cc_final: 0.7741 (tm-30) REVERT: B 693 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9072 (tp) outliers start: 102 outliers final: 71 residues processed: 246 average time/residue: 0.0887 time to fit residues: 35.1650 Evaluate side-chains 241 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 160 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 747 ASP Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 896 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 111 ASN B 113 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.150088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.094896 restraints weight = 27257.373| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.74 r_work: 0.3491 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13898 Z= 0.154 Angle : 0.692 12.305 18822 Z= 0.347 Chirality : 0.045 0.342 2268 Planarity : 0.005 0.061 2338 Dihedral : 8.428 59.046 1980 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.41 % Favored : 90.85 % Rotamer: Outliers : 6.73 % Allowed : 26.45 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.20), residues: 1760 helix: 0.18 (0.17), residues: 913 sheet: 0.02 (0.45), residues: 142 loop : -2.22 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 627 TYR 0.014 0.002 TYR B 397 PHE 0.017 0.001 PHE B 776 TRP 0.009 0.001 TRP B 302 HIS 0.004 0.001 HIS B 869 Details of bonding type rmsd covalent geometry : bond 0.00353 (13898) covalent geometry : angle 0.69240 (18822) hydrogen bonds : bond 0.03712 ( 692) hydrogen bonds : angle 4.83320 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 167 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 231 MET cc_start: 0.8334 (mtp) cc_final: 0.8117 (mtp) REVERT: A 377 LEU cc_start: 0.8935 (tp) cc_final: 0.8425 (tp) REVERT: A 407 LEU cc_start: 0.9502 (tp) cc_final: 0.9283 (mm) REVERT: A 471 MET cc_start: 0.7651 (ppp) cc_final: 0.7296 (ptp) REVERT: A 475 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6597 (t) REVERT: A 571 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8750 (mmmm) REVERT: A 638 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8243 (p0) REVERT: A 656 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: A 806 TYR cc_start: 0.7479 (t80) cc_final: 0.6942 (t80) REVERT: A 856 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 879 ASN cc_start: 0.8700 (t0) cc_final: 0.8443 (t0) REVERT: B 91 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: B 146 MET cc_start: 0.7145 (pmm) cc_final: 0.6863 (pmm) REVERT: B 373 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 374 MET cc_start: 0.8279 (mmm) cc_final: 0.8072 (mmp) REVERT: B 430 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 542 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8687 (p0) REVERT: B 546 GLU cc_start: 0.8365 (pm20) cc_final: 0.7728 (tm-30) REVERT: B 684 GLU cc_start: 0.8292 (tp30) cc_final: 0.7895 (tp30) REVERT: B 693 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9032 (tp) REVERT: B 841 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.9022 (mt0) REVERT: B 854 MET cc_start: 0.8565 (mpp) cc_final: 0.8259 (mmt) REVERT: B 856 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7190 (tp) outliers start: 102 outliers final: 61 residues processed: 250 average time/residue: 0.0831 time to fit residues: 33.7880 Evaluate side-chains 236 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 747 ASP Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 841 GLN Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 896 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 128 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 111 ASN B 113 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.149968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094692 restraints weight = 27379.636| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.73 r_work: 0.3435 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13898 Z= 0.166 Angle : 0.692 12.165 18822 Z= 0.345 Chirality : 0.045 0.341 2268 Planarity : 0.005 0.060 2338 Dihedral : 8.260 57.837 1973 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.47 % Favored : 90.85 % Rotamer: Outliers : 7.19 % Allowed : 25.53 % Favored : 67.28 % 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: -1.10 (0.20), residues: 1760 helix: 0.22 (0.17), residues: 922 sheet: 0.01 (0.46), residues: 143 loop : -2.20 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.013 0.002 TYR B 689 PHE 0.022 0.001 PHE A 392 TRP 0.009 0.001 TRP B 302 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00387 (13898) covalent geometry : angle 0.69237 (18822) hydrogen bonds : bond 0.03648 ( 692) hydrogen bonds : angle 4.77294 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 167 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8278 (mtp) cc_final: 0.8038 (mtp) REVERT: A 263 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.6965 (p0) REVERT: A 377 LEU cc_start: 0.8998 (tp) cc_final: 0.8477 (tp) REVERT: A 407 LEU cc_start: 0.9556 (tp) cc_final: 0.9304 (mm) REVERT: A 490 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: A 571 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8771 (mmmm) REVERT: A 638 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (p0) REVERT: A 656 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: A 806 TYR cc_start: 0.7540 (t80) cc_final: 0.6953 (t80) REVERT: A 856 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 879 ASN cc_start: 0.8744 (t0) cc_final: 0.8483 (t0) REVERT: B 91 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: B 373 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7466 (mm) REVERT: B 374 MET cc_start: 0.8332 (mmm) cc_final: 0.8016 (mmm) REVERT: B 430 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.7031 (t80) REVERT: B 542 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8639 (p0) REVERT: B 546 GLU cc_start: 0.8449 (pm20) cc_final: 0.7744 (tm-30) REVERT: B 684 GLU cc_start: 0.8281 (tp30) cc_final: 0.7874 (tp30) REVERT: B 693 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9048 (tp) REVERT: B 736 PHE cc_start: 0.8532 (m-10) cc_final: 0.8311 (m-10) REVERT: B 854 MET cc_start: 0.8564 (mpp) cc_final: 0.8277 (mmt) REVERT: B 856 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7203 (tp) outliers start: 109 outliers final: 74 residues processed: 256 average time/residue: 0.0890 time to fit residues: 36.9675 Evaluate side-chains 248 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 162 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 747 ASP Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 896 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 0.0970 chunk 106 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 169 optimal weight: 0.0970 chunk 90 optimal weight: 20.0000 chunk 164 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.152548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.098340 restraints weight = 27236.303| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.71 r_work: 0.3504 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13898 Z= 0.122 Angle : 0.689 14.709 18822 Z= 0.340 Chirality : 0.044 0.317 2268 Planarity : 0.004 0.062 2338 Dihedral : 7.871 57.229 1970 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.84 % Favored : 91.48 % Rotamer: Outliers : 5.47 % Allowed : 27.51 % Favored : 67.02 % 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: -0.93 (0.20), residues: 1760 helix: 0.39 (0.18), residues: 919 sheet: 0.17 (0.46), residues: 144 loop : -2.20 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.013 0.001 TYR B 396 PHE 0.027 0.001 PHE A 776 TRP 0.010 0.001 TRP B 302 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00262 (13898) covalent geometry : angle 0.68918 (18822) hydrogen bonds : bond 0.03336 ( 692) hydrogen bonds : angle 4.60910 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 169 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8288 (mtp) cc_final: 0.8075 (mtp) REVERT: A 377 LEU cc_start: 0.9038 (tp) cc_final: 0.8538 (tp) REVERT: A 392 PHE cc_start: 0.8426 (t80) cc_final: 0.8057 (t80) REVERT: A 407 LEU cc_start: 0.9572 (tp) cc_final: 0.9318 (mm) REVERT: A 490 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: A 500 ASP cc_start: 0.9053 (p0) cc_final: 0.8610 (t0) REVERT: A 571 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8826 (mmmm) REVERT: A 638 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8089 (p0) REVERT: A 656 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 820 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8671 (tm-30) REVERT: A 879 ASN cc_start: 0.8597 (t0) cc_final: 0.8377 (t0) REVERT: B 91 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 111 ASN cc_start: 0.5748 (OUTLIER) cc_final: 0.5366 (t160) REVERT: B 320 MET cc_start: 0.8158 (mmp) cc_final: 0.7937 (mmp) REVERT: B 373 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 374 MET cc_start: 0.8345 (mmm) cc_final: 0.8048 (mmm) REVERT: B 430 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.7046 (t80) REVERT: B 542 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8631 (p0) REVERT: B 546 GLU cc_start: 0.8399 (pm20) cc_final: 0.7709 (tm-30) REVERT: B 684 GLU cc_start: 0.8178 (tp30) cc_final: 0.7758 (tp30) REVERT: B 733 ILE cc_start: 0.9210 (tp) cc_final: 0.8959 (mt) REVERT: B 736 PHE cc_start: 0.8470 (m-10) cc_final: 0.8267 (m-10) outliers start: 83 outliers final: 56 residues processed: 234 average time/residue: 0.0885 time to fit residues: 33.1174 Evaluate side-chains 227 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 897 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 617 GLN B 295 ASN B 461 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.152241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098490 restraints weight = 27468.012| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.71 r_work: 0.3502 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13898 Z= 0.127 Angle : 0.697 14.994 18822 Z= 0.341 Chirality : 0.044 0.314 2268 Planarity : 0.004 0.061 2338 Dihedral : 7.642 58.968 1966 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.67 % Favored : 91.65 % Rotamer: Outliers : 5.61 % Allowed : 28.10 % Favored : 66.29 % 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: -0.82 (0.20), residues: 1760 helix: 0.48 (0.18), residues: 913 sheet: 0.27 (0.46), residues: 144 loop : -2.12 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.012 0.001 TYR B 806 PHE 0.047 0.001 PHE B 776 TRP 0.009 0.001 TRP B 302 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00282 (13898) covalent geometry : angle 0.69715 (18822) hydrogen bonds : bond 0.03290 ( 692) hydrogen bonds : angle 4.57605 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 168 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8049 (tp) cc_final: 0.7757 (tp) REVERT: A 231 MET cc_start: 0.8271 (mtp) cc_final: 0.8053 (mtp) REVERT: A 263 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 377 LEU cc_start: 0.9054 (tp) cc_final: 0.8541 (tp) REVERT: A 392 PHE cc_start: 0.8457 (t80) cc_final: 0.8134 (t80) REVERT: A 407 LEU cc_start: 0.9570 (tp) cc_final: 0.9308 (mm) REVERT: A 490 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: A 571 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8811 (mmmm) REVERT: A 638 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8108 (p0) REVERT: A 820 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 879 ASN cc_start: 0.8560 (t0) cc_final: 0.8341 (t0) REVERT: B 91 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 373 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7320 (mm) REVERT: B 374 MET cc_start: 0.8342 (mmm) cc_final: 0.8120 (mmm) REVERT: B 430 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.7078 (t80) REVERT: B 542 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8677 (p0) REVERT: B 546 GLU cc_start: 0.8366 (pm20) cc_final: 0.7686 (tm-30) REVERT: B 684 GLU cc_start: 0.8202 (tp30) cc_final: 0.7786 (tp30) outliers start: 85 outliers final: 55 residues processed: 235 average time/residue: 0.0863 time to fit residues: 33.0382 Evaluate side-chains 224 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 123 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 111 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN ** B 814 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.150082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.095154 restraints weight = 27181.310| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.74 r_work: 0.3432 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13898 Z= 0.182 Angle : 0.735 16.163 18822 Z= 0.359 Chirality : 0.046 0.336 2268 Planarity : 0.005 0.060 2338 Dihedral : 7.723 58.370 1965 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.30 % Favored : 91.02 % Rotamer: Outliers : 5.67 % Allowed : 28.30 % Favored : 66.03 % 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: -0.85 (0.20), residues: 1760 helix: 0.43 (0.18), residues: 912 sheet: 0.27 (0.46), residues: 144 loop : -2.10 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 77 TYR 0.014 0.002 TYR B 689 PHE 0.048 0.002 PHE B 776 TRP 0.009 0.001 TRP B 302 HIS 0.004 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00427 (13898) covalent geometry : angle 0.73511 (18822) hydrogen bonds : bond 0.03632 ( 692) hydrogen bonds : angle 4.66852 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8300 (mtp) cc_final: 0.8099 (mtp) REVERT: A 263 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6963 (p0) REVERT: A 377 LEU cc_start: 0.8986 (tp) cc_final: 0.8471 (tp) REVERT: A 392 PHE cc_start: 0.8364 (t80) cc_final: 0.8097 (t80) REVERT: A 407 LEU cc_start: 0.9549 (tp) cc_final: 0.9300 (mm) REVERT: A 490 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: A 500 ASP cc_start: 0.9024 (p0) cc_final: 0.8658 (t0) REVERT: A 571 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9123 (mmmm) REVERT: A 638 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8096 (p0) REVERT: A 879 ASN cc_start: 0.8602 (t0) cc_final: 0.8393 (t0) REVERT: B 91 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: B 111 ASN cc_start: 0.5809 (OUTLIER) cc_final: 0.5328 (t160) REVERT: B 299 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7265 (pttp) REVERT: B 373 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7340 (mm) REVERT: B 374 MET cc_start: 0.8306 (mmm) cc_final: 0.7999 (mmm) REVERT: B 430 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 542 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8688 (p0) REVERT: B 546 GLU cc_start: 0.8301 (pm20) cc_final: 0.7667 (tm-30) REVERT: B 684 GLU cc_start: 0.8314 (tp30) cc_final: 0.7946 (tp30) outliers start: 86 outliers final: 61 residues processed: 232 average time/residue: 0.0879 time to fit residues: 32.4654 Evaluate side-chains 227 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 143 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 617 GLN B 111 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.147985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092520 restraints weight = 27373.753| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.75 r_work: 0.3389 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13898 Z= 0.243 Angle : 0.788 17.975 18822 Z= 0.384 Chirality : 0.048 0.362 2268 Planarity : 0.005 0.069 2338 Dihedral : 7.828 58.753 1963 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.58 % Favored : 90.68 % Rotamer: Outliers : 6.20 % Allowed : 27.97 % Favored : 65.83 % 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: -0.96 (0.20), residues: 1760 helix: 0.31 (0.17), residues: 912 sheet: -0.18 (0.45), residues: 151 loop : -2.03 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.014 0.002 TYR B 689 PHE 0.049 0.002 PHE B 776 TRP 0.008 0.001 TRP A 302 HIS 0.004 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00578 (13898) covalent geometry : angle 0.78784 (18822) hydrogen bonds : bond 0.03937 ( 692) hydrogen bonds : angle 4.84952 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 155 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8255 (mtp) cc_final: 0.8043 (mtp) REVERT: A 263 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6944 (p0) REVERT: A 377 LEU cc_start: 0.9002 (tp) cc_final: 0.8487 (tp) REVERT: A 392 PHE cc_start: 0.8407 (t80) cc_final: 0.8115 (t80) REVERT: A 407 LEU cc_start: 0.9575 (tp) cc_final: 0.9330 (mm) REVERT: A 500 ASP cc_start: 0.9013 (p0) cc_final: 0.8687 (t0) REVERT: A 571 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8802 (mmmm) REVERT: A 638 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 806 TYR cc_start: 0.7573 (t80) cc_final: 0.7003 (t80) REVERT: A 879 ASN cc_start: 0.8765 (t0) cc_final: 0.8490 (t0) REVERT: B 91 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: B 299 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (pttp) REVERT: B 373 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7357 (mm) REVERT: B 374 MET cc_start: 0.8304 (mmm) cc_final: 0.7996 (mmm) REVERT: B 542 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8646 (p0) REVERT: B 546 GLU cc_start: 0.8407 (pm20) cc_final: 0.7735 (tm-30) REVERT: B 693 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9099 (tp) outliers start: 94 outliers final: 73 residues processed: 231 average time/residue: 0.0823 time to fit residues: 30.5227 Evaluate side-chains 230 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 149 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 747 ASP Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 896 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 111 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096184 restraints weight = 27330.459| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.77 r_work: 0.3467 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13898 Z= 0.147 Angle : 0.751 19.794 18822 Z= 0.363 Chirality : 0.046 0.330 2268 Planarity : 0.005 0.062 2338 Dihedral : 7.651 59.875 1963 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.41 % Favored : 90.91 % Rotamer: Outliers : 4.88 % Allowed : 29.29 % Favored : 65.83 % 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: -0.88 (0.20), residues: 1760 helix: 0.38 (0.17), residues: 914 sheet: 0.25 (0.45), residues: 145 loop : -2.08 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.012 0.002 TYR B 806 PHE 0.038 0.001 PHE B 776 TRP 0.013 0.001 TRP B 817 HIS 0.003 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00339 (13898) covalent geometry : angle 0.75126 (18822) hydrogen bonds : bond 0.03504 ( 692) hydrogen bonds : angle 4.69126 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8059 (tp) cc_final: 0.7698 (mt) REVERT: A 231 MET cc_start: 0.8218 (mtp) cc_final: 0.8012 (mtp) REVERT: A 263 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6989 (p0) REVERT: A 377 LEU cc_start: 0.9048 (tp) cc_final: 0.8539 (tp) REVERT: A 392 PHE cc_start: 0.8411 (t80) cc_final: 0.8093 (t80) REVERT: A 407 LEU cc_start: 0.9589 (tp) cc_final: 0.9324 (mm) REVERT: A 490 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: A 500 ASP cc_start: 0.9038 (p0) cc_final: 0.8723 (t0) REVERT: A 571 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8832 (mmmm) REVERT: A 638 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8154 (p0) REVERT: A 820 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 879 ASN cc_start: 0.8667 (t0) cc_final: 0.8423 (t0) REVERT: B 91 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: B 111 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5224 (t160) REVERT: B 373 LEU cc_start: 0.8139 (mm) cc_final: 0.7367 (mm) REVERT: B 374 MET cc_start: 0.8279 (mmm) cc_final: 0.7999 (mmm) REVERT: B 397 TYR cc_start: 0.7140 (m-80) cc_final: 0.6907 (m-80) REVERT: B 542 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8613 (p0) REVERT: B 546 GLU cc_start: 0.8397 (pm20) cc_final: 0.7722 (tm-30) REVERT: B 684 GLU cc_start: 0.8309 (tp30) cc_final: 0.7908 (tp30) outliers start: 74 outliers final: 58 residues processed: 216 average time/residue: 0.0871 time to fit residues: 30.3488 Evaluate side-chains 215 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 150 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 895 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.149876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.094997 restraints weight = 27326.882| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.76 r_work: 0.3440 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13898 Z= 0.186 Angle : 0.765 18.550 18822 Z= 0.369 Chirality : 0.047 0.336 2268 Planarity : 0.005 0.061 2338 Dihedral : 7.630 59.755 1961 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.52 % Favored : 90.85 % Rotamer: Outliers : 5.08 % Allowed : 28.83 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1760 helix: 0.38 (0.17), residues: 911 sheet: 0.23 (0.45), residues: 145 loop : -2.10 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.013 0.002 TYR B 806 PHE 0.033 0.002 PHE A 776 TRP 0.008 0.001 TRP B 817 HIS 0.004 0.001 HIS B 726 Details of bonding type rmsd covalent geometry : bond 0.00441 (13898) covalent geometry : angle 0.76494 (18822) hydrogen bonds : bond 0.03590 ( 692) hydrogen bonds : angle 4.71383 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.54 seconds wall clock time: 64 minutes 10.17 seconds (3850.17 seconds total)