Starting phenix.real_space_refine on Thu Aug 6 09:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7v_18992/08_2026/8r7v_18992.map" } resolution = 3.12 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= 0.024 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: 7 Type Number sf(0) Gaussians P 58 5.49 5 Mg 1 5.21 5 S 64 5.16 5 C 9124 2.51 5 N 2513 2.21 5 O 2869 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6750 Classifications: {'peptide': 853} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 827} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6664 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 833, 6661 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 25, 'TRANS': 807} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 833, 6661 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 25, 'TRANS': 807} Chain breaks: 4 bond proxies already assigned to first conformer: 6778 Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'SO4': 1, 'YKQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.97, per 1000 atoms: 0.27 Number of scatterers: 14630 At special positions: 0 Unit cell: (86.849, 115.189, 174.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 64 16.00 P 58 15.00 Mg 1 11.99 F 1 9.00 O 2869 8.00 N 2513 7.00 C 9124 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: 1.63 Conformation dependent library (CDL) restraints added in 840.9 milliseconds 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 53.4% alpha, 13.1% beta 24 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.585A pdb=" N VAL A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.769A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.511A pdb=" N ASP A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.843A pdb=" N GLU A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.829A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.069A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 424 removed outlier: 3.577A pdb=" N CYS A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Proline residue: A 415 - end of helix removed outlier: 3.567A pdb=" N GLU A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N HIS A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 475 through 504 Processing helix chain 'A' and resid 529 through 534 removed outlier: 4.339A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 587 removed outlier: 3.636A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 614 removed outlier: 3.607A pdb=" N MET A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.690A pdb=" N VAL A 644 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.551A pdb=" N ALA A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 905 through 919 Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.718A pdb=" N GLU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.753A pdb=" N LYS B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 312 through 317' Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.675A pdb=" N VAL B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 464 through 476 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.595A pdb=" N ILE B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 493 " --> pdb=" O SER B 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 493' Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.583A pdb=" N ASN B 524 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 655 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 673 through 679 removed outlier: 4.562A pdb=" N GLU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 687 removed outlier: 3.831A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 709 through 738 removed outlier: 3.536A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 843 Processing helix chain 'B' and resid 864 through 872 removed outlier: 3.807A pdb=" N GLY B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 removed outlier: 3.708A pdb=" N ILE B 906 " --> pdb=" O LYS B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 966 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.875A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1079 through 1113 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.594A pdb=" N VAL A 34 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 103 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 100 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 122 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 102 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 152 removed outlier: 4.828A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A 159 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.056A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASP A 748 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 711 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEU A 805 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 814 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.700A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.816A pdb=" N CYS A 697 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 637 " --> pdb=" O CYS A 697 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 631 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 633 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 657 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS A 635 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 655 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.684A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLN B 309 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLU B 251 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AB1, first strand: chain 'B' and resid 454 through 458 removed outlier: 3.530A pdb=" N LEU B 428 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 367 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU B 426 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 369 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU B 428 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 371 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 400 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 754 through 757 removed outlier: 7.003A pdb=" N VAL B 777 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 773 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 779 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 771 " --> pdb=" O ARG B 779 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 880 through 884 removed outlier: 5.264A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 935 through 938 removed outlier: 6.434A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET B1030 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1027 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B1060 " --> pdb=" O ASN B1027 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N HIS B1029 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN B1058 " --> pdb=" O HIS B1029 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4041 1.34 - 1.46: 4138 1.46 - 1.58: 6602 1.58 - 1.71: 112 1.71 - 1.83: 101 Bond restraints: 14994 Sorted by residual: bond pdb=" C ALA A 710 " pdb=" N ARG A 711 " ideal model delta sigma weight residual 1.332 1.419 -0.087 1.26e-02 6.30e+03 4.82e+01 bond pdb=" C ARG A 711 " pdb=" N VAL A 712 " ideal model delta sigma weight residual 1.329 1.416 -0.087 1.40e-02 5.10e+03 3.86e+01 bond pdb=" C4 ADP A2001 " pdb=" C5 ADP A2001 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C5 ADP A2001 " pdb=" C6 ADP A2001 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C ILE B 736 " pdb=" N LEU B 737 " ideal model delta sigma weight residual 1.335 1.387 -0.052 1.38e-02 5.25e+03 1.45e+01 ... (remaining 14989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 19945 2.39 - 4.79: 480 4.79 - 7.18: 33 7.18 - 9.57: 8 9.57 - 11.97: 2 Bond angle restraints: 20468 Sorted by residual: angle pdb=" CB GLU B 725 " pdb=" CG GLU B 725 " pdb=" CD GLU B 725 " ideal model delta sigma weight residual 112.60 120.54 -7.94 1.70e+00 3.46e-01 2.18e+01 angle pdb=" CA ASP A 446 " pdb=" CB ASP A 446 " pdb=" CG ASP A 446 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" O ALA A 710 " pdb=" C ALA A 710 " pdb=" N ARG A 711 " ideal model delta sigma weight residual 123.24 128.56 -5.32 1.23e+00 6.61e-01 1.87e+01 angle pdb=" N PRO B1012 " pdb=" CA PRO B1012 " pdb=" C PRO B1012 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.80e+01 angle pdb=" O ILE B 736 " pdb=" C ILE B 736 " pdb=" N LEU B 737 " ideal model delta sigma weight residual 121.83 126.07 -4.24 1.03e+00 9.43e-01 1.69e+01 ... (remaining 20463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 7704 23.04 - 46.08: 966 46.08 - 69.12: 285 69.12 - 92.15: 23 92.15 - 115.19: 1 Dihedral angle restraints: 8979 sinusoidal: 4054 harmonic: 4925 Sorted by residual: dihedral pdb=" O1B ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PB ADP A2001 " pdb=" PA ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 -175.19 115.19 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" CA THR B 746 " pdb=" C THR B 746 " pdb=" N VAL B 747 " pdb=" CA VAL B 747 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA CYS A 707 " pdb=" C CYS A 707 " pdb=" N ILE A 708 " pdb=" CA ILE A 708 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 8976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1285 0.062 - 0.123: 832 0.123 - 0.185: 198 0.185 - 0.246: 21 0.246 - 0.308: 5 Chirality restraints: 2341 Sorted by residual: chirality pdb=" P DG C 16 " pdb=" OP1 DG C 16 " pdb=" OP2 DG C 16 " pdb=" O5' DG C 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.64 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" P DG C 26 " pdb=" OP1 DG C 26 " pdb=" OP2 DG C 26 " pdb=" O5' DG C 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.63 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" P DG C 21 " pdb=" OP1 DG C 21 " pdb=" OP2 DG C 21 " pdb=" O5' DG C 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.62 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2338 not shown) Planarity restraints: 2407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 711 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ARG A 711 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 711 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 712 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 YKQ B1201 " -0.006 2.00e-02 2.50e+03 1.03e-02 2.14e+00 pdb=" C24 YKQ B1201 " 0.006 2.00e-02 2.50e+03 pdb=" C25 YKQ B1201 " 0.001 2.00e-02 2.50e+03 pdb=" C26 YKQ B1201 " 0.001 2.00e-02 2.50e+03 pdb=" C27 YKQ B1201 " -0.019 2.00e-02 2.50e+03 pdb=" C33 YKQ B1201 " -0.007 2.00e-02 2.50e+03 pdb=" N28 YKQ B1201 " 0.017 2.00e-02 2.50e+03 pdb=" O22 YKQ B1201 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1078 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C VAL B1078 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL B1078 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO B1079 " 0.008 2.00e-02 2.50e+03 ... (remaining 2404 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 111 2.56 - 3.14: 11381 3.14 - 3.73: 24826 3.73 - 4.31: 32700 4.31 - 4.90: 53220 Nonbonded interactions: 122238 Sorted by model distance: nonbonded pdb="MG MG A2000 " pdb=" O3B ADP A2001 " model vdw 1.971 2.170 nonbonded pdb=" O ASP A 654 " pdb=" OH TYR A 678 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR B 236 " pdb=" OD2 ASP B 262 " model vdw 2.185 3.040 nonbonded pdb=" O SER A 738 " pdb=" OG SER A 738 " model vdw 2.211 3.040 nonbonded pdb=" NH1 ARG B 855 " pdb=" O SER B 968 " model vdw 2.221 3.120 ... (remaining 122233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.720 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 14994 Z= 0.448 Angle : 0.974 11.966 20468 Z= 0.622 Chirality : 0.076 0.308 2341 Planarity : 0.004 0.033 2407 Dihedral : 20.373 115.192 5781 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.42 % Allowed : 28.09 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1661 helix: 1.33 (0.18), residues: 806 sheet: -0.58 (0.36), residues: 215 loop : -1.16 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 752 TYR 0.015 0.003 TYR A 121 PHE 0.019 0.003 PHE A 777 TRP 0.012 0.003 TRP A 764 HIS 0.012 0.003 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.45 (14994) covalent geometry : angle 0.97405 / 0.62 (20468) hydrogen bonds : bond 0.12740 / 8.74 ( 774) hydrogen bonds : angle 5.53282 / 3.81 ( 2143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 341 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.8114 (pm20) cc_final: 0.7642 (mp0) REVERT: A 392 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7125 (ttmm) REVERT: A 569 GLU cc_start: 0.7625 (mp0) cc_final: 0.7391 (mp0) REVERT: B 269 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 318 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 474 GLU cc_start: 0.7822 (tp30) cc_final: 0.7570 (tp30) REVERT: B 802 ASP cc_start: 0.8239 (m-30) cc_final: 0.7976 (t0) REVERT: B 832 ASP cc_start: 0.7608 (t70) cc_final: 0.7055 (t0) REVERT: B 938 ARG cc_start: 0.7340 (tpt170) cc_final: 0.6984 (tpt170) outliers start: 35 outliers final: 19 residues processed: 360 average time/residue: 0.1381 time to fit residues: 71.5061 Evaluate side-chains 353 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 875 ASP Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 242 ASN A 263 ASN A 409 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 596 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140120 restraints weight = 22408.083| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.26 r_work: 0.3617 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14994 Z= 0.160 Angle : 0.619 8.614 20468 Z= 0.326 Chirality : 0.042 0.160 2341 Planarity : 0.004 0.049 2407 Dihedral : 17.829 104.198 2485 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.42 % Allowed : 28.56 % Favored : 69.02 % 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: 0.27 (0.21), residues: 1661 helix: 1.36 (0.18), residues: 815 sheet: -0.70 (0.35), residues: 226 loop : -1.02 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 711 TYR 0.011 0.001 TYR A 408 PHE 0.019 0.002 PHE B 469 TRP 0.009 0.001 TRP A 764 HIS 0.010 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (14994) covalent geometry : angle 0.61887 / 0.33 (20468) hydrogen bonds : bond 0.04540 / 2.99 ( 774) hydrogen bonds : angle 4.68861 / 3.29 ( 2143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8336 (mppt) cc_final: 0.8087 (mppt) REVERT: A 371 GLU cc_start: 0.7289 (pm20) cc_final: 0.6944 (pm20) REVERT: A 382 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7292 (ttp-110) REVERT: A 501 ARG cc_start: 0.3268 (OUTLIER) cc_final: 0.2606 (ptm-80) REVERT: A 569 GLU cc_start: 0.7318 (mp0) cc_final: 0.7029 (mp0) REVERT: A 691 ILE cc_start: 0.8110 (pt) cc_final: 0.7853 (pt) REVERT: B 269 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6652 (mm-30) REVERT: B 568 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7880 (mtmm) REVERT: B 832 ASP cc_start: 0.7786 (t70) cc_final: 0.7105 (t0) REVERT: B 889 GLU cc_start: 0.7301 (pt0) cc_final: 0.7084 (pt0) REVERT: B 961 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7508 (mm-30) outliers start: 35 outliers final: 24 residues processed: 342 average time/residue: 0.1356 time to fit residues: 66.6530 Evaluate side-chains 338 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 875 ASP Chi-restraints excluded: chain B residue 963 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 168 optimal weight: 40.0000 chunk 10 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 750 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 = 0.4222 r_free = 0.4222 target = 0.178173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140508 restraints weight = 25049.312| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.44 r_work: 0.3599 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14994 Z= 0.153 Angle : 0.591 8.286 20468 Z= 0.311 Chirality : 0.041 0.161 2341 Planarity : 0.004 0.053 2407 Dihedral : 17.732 99.722 2451 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.49 % Allowed : 27.69 % Favored : 68.82 % 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: 0.24 (0.21), residues: 1661 helix: 1.32 (0.18), residues: 816 sheet: -0.69 (0.35), residues: 228 loop : -1.01 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 938 TYR 0.012 0.001 TYR A 656 PHE 0.013 0.001 PHE B 291 TRP 0.007 0.001 TRP A 764 HIS 0.014 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (14994) covalent geometry : angle 0.59065 / 0.31 (20468) hydrogen bonds : bond 0.04156 / 2.72 ( 774) hydrogen bonds : angle 4.54167 / 3.20 ( 2143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6464 (mtt90) cc_final: 0.6199 (mtt90) REVERT: A 229 LYS cc_start: 0.8323 (mppt) cc_final: 0.8068 (mppt) REVERT: A 274 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6918 (tp) REVERT: A 371 GLU cc_start: 0.7309 (pm20) cc_final: 0.6855 (mp0) REVERT: A 501 ARG cc_start: 0.3141 (OUTLIER) cc_final: 0.2522 (ptm-80) REVERT: B 269 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6660 (mm-30) REVERT: B 677 GLU cc_start: 0.7652 (tp30) cc_final: 0.7394 (tp30) REVERT: B 832 ASP cc_start: 0.7787 (t70) cc_final: 0.7278 (t0) REVERT: B 889 GLU cc_start: 0.7289 (pt0) cc_final: 0.7062 (pt0) REVERT: B 938 ARG cc_start: 0.7253 (tpt170) cc_final: 0.6829 (tpt170) REVERT: B 955 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: B 961 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7543 (mm-30) outliers start: 51 outliers final: 28 residues processed: 342 average time/residue: 0.1362 time to fit residues: 66.7741 Evaluate side-chains 336 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 23 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 127 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 170 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 544 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139622 restraints weight = 22647.457| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.27 r_work: 0.3601 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14994 Z= 0.192 Angle : 0.614 8.784 20468 Z= 0.321 Chirality : 0.042 0.165 2341 Planarity : 0.004 0.056 2407 Dihedral : 17.717 97.201 2449 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.63 % Allowed : 27.35 % Favored : 69.02 % 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: 0.17 (0.21), residues: 1661 helix: 1.23 (0.18), residues: 815 sheet: -0.73 (0.34), residues: 226 loop : -1.00 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 616 TYR 0.011 0.001 TYR B1068 PHE 0.031 0.002 PHE A 447 TRP 0.008 0.001 TRP B 807 HIS 0.008 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (14994) covalent geometry : angle 0.61389 / 0.32 (20468) hydrogen bonds : bond 0.04151 / 2.70 ( 774) hydrogen bonds : angle 4.51371 / 3.18 ( 2143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 81 SER cc_start: 0.8673 (p) cc_final: 0.8398 (t) REVERT: A 171 ARG cc_start: 0.6485 (mtt90) cc_final: 0.6211 (mtt90) REVERT: A 188 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 229 LYS cc_start: 0.8333 (mppt) cc_final: 0.8073 (mppt) REVERT: A 274 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6921 (tp) REVERT: A 371 GLU cc_start: 0.7262 (pm20) cc_final: 0.6862 (mp0) REVERT: A 381 LEU cc_start: 0.8294 (mt) cc_final: 0.8063 (mt) REVERT: A 383 ARG cc_start: 0.7323 (mtt90) cc_final: 0.6953 (mtm110) REVERT: A 501 ARG cc_start: 0.3149 (OUTLIER) cc_final: 0.2516 (ptm-80) REVERT: A 592 MET cc_start: 0.7299 (mmm) cc_final: 0.6985 (mtp) REVERT: A 701 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: B 405 PHE cc_start: 0.8164 (p90) cc_final: 0.7963 (p90) REVERT: B 543 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7755 (mtm110) REVERT: B 544 ASN cc_start: 0.7818 (m-40) cc_final: 0.7611 (m110) REVERT: B 568 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7943 (mtmm) REVERT: B 677 GLU cc_start: 0.7621 (tp30) cc_final: 0.7364 (tp30) REVERT: B 753 MET cc_start: 0.4184 (mmp) cc_final: 0.3966 (mmm) REVERT: B 832 ASP cc_start: 0.7781 (t70) cc_final: 0.7108 (t0) REVERT: B 889 GLU cc_start: 0.7222 (pt0) cc_final: 0.6968 (pt0) REVERT: B 938 ARG cc_start: 0.7273 (tpt170) cc_final: 0.7026 (tpt170) outliers start: 53 outliers final: 35 residues processed: 348 average time/residue: 0.1225 time to fit residues: 61.6733 Evaluate side-chains 346 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 36 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** 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 = 0.4213 r_free = 0.4213 target = 0.176412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137933 restraints weight = 30469.694| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.78 r_work: 0.3562 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14994 Z= 0.166 Angle : 0.589 8.970 20468 Z= 0.311 Chirality : 0.041 0.174 2341 Planarity : 0.004 0.050 2407 Dihedral : 17.655 95.214 2446 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.56 % Allowed : 28.02 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1661 helix: 1.24 (0.18), residues: 817 sheet: -0.77 (0.34), residues: 226 loop : -0.99 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 752 TYR 0.012 0.001 TYR A 408 PHE 0.023 0.002 PHE A 447 TRP 0.007 0.001 TRP A 764 HIS 0.007 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (14994) covalent geometry : angle 0.58941 / 0.31 (20468) hydrogen bonds : bond 0.03988 / 2.60 ( 774) hydrogen bonds : angle 4.45581 / 3.14 ( 2143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8304 (p) REVERT: A 81 SER cc_start: 0.8672 (p) cc_final: 0.8423 (t) REVERT: A 171 ARG cc_start: 0.6571 (mtt90) cc_final: 0.6106 (mtt90) REVERT: A 188 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 229 LYS cc_start: 0.8339 (mppt) cc_final: 0.8131 (mppt) REVERT: A 274 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7010 (tp) REVERT: A 371 GLU cc_start: 0.7370 (pm20) cc_final: 0.6969 (mp0) REVERT: A 501 ARG cc_start: 0.3214 (OUTLIER) cc_final: 0.2597 (ptm-80) REVERT: A 592 MET cc_start: 0.7280 (mmm) cc_final: 0.7006 (mtp) REVERT: A 701 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: B 405 PHE cc_start: 0.8177 (p90) cc_final: 0.7943 (p90) REVERT: B 544 ASN cc_start: 0.7851 (m-40) cc_final: 0.7595 (m-40) REVERT: B 677 GLU cc_start: 0.7695 (tp30) cc_final: 0.7420 (tp30) REVERT: B 938 ARG cc_start: 0.7292 (tpt170) cc_final: 0.7085 (tpt170) REVERT: B 968 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8427 (t) outliers start: 52 outliers final: 38 residues processed: 352 average time/residue: 0.1270 time to fit residues: 64.9319 Evaluate side-chains 356 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 91 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 chunk 166 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.178035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141525 restraints weight = 22957.008| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.32 r_work: 0.3618 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14994 Z= 0.141 Angle : 0.596 9.154 20468 Z= 0.311 Chirality : 0.041 0.169 2341 Planarity : 0.004 0.051 2407 Dihedral : 17.614 91.336 2446 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.56 % Allowed : 28.23 % Favored : 68.21 % 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: 0.23 (0.21), residues: 1661 helix: 1.30 (0.18), residues: 817 sheet: -0.79 (0.34), residues: 226 loop : -0.97 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 752 TYR 0.011 0.001 TYR A 408 PHE 0.021 0.001 PHE A 447 TRP 0.008 0.001 TRP A 764 HIS 0.009 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14994) covalent geometry : angle 0.59586 / 0.31 (20468) hydrogen bonds : bond 0.03861 / 2.51 ( 774) hydrogen bonds : angle 4.39418 / 3.10 ( 2143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 81 SER cc_start: 0.8618 (p) cc_final: 0.8379 (t) REVERT: A 171 ARG cc_start: 0.6468 (mtt90) cc_final: 0.6048 (mtt90) REVERT: A 188 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 229 LYS cc_start: 0.8288 (mppt) cc_final: 0.8055 (mppt) REVERT: A 274 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6916 (tp) REVERT: A 371 GLU cc_start: 0.7239 (pm20) cc_final: 0.6831 (mp0) REVERT: A 383 ARG cc_start: 0.7295 (mtt90) cc_final: 0.6955 (mtm110) REVERT: A 501 ARG cc_start: 0.3114 (OUTLIER) cc_final: 0.2520 (ptm-80) REVERT: A 592 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6986 (mtp) REVERT: A 701 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: B 261 GLU cc_start: 0.7567 (pm20) cc_final: 0.7064 (pm20) REVERT: B 264 GLU cc_start: 0.7357 (mp0) cc_final: 0.6856 (mp0) REVERT: B 405 PHE cc_start: 0.8164 (p90) cc_final: 0.7924 (p90) REVERT: B 544 ASN cc_start: 0.7767 (m-40) cc_final: 0.7531 (m110) REVERT: B 677 GLU cc_start: 0.7635 (tp30) cc_final: 0.7364 (tp30) REVERT: B 832 ASP cc_start: 0.7740 (t70) cc_final: 0.7301 (t0) REVERT: B 854 GLU cc_start: 0.7839 (pm20) cc_final: 0.7296 (mp0) REVERT: B 889 GLU cc_start: 0.7233 (pt0) cc_final: 0.6951 (pt0) REVERT: B 918 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7504 (pt) outliers start: 52 outliers final: 37 residues processed: 354 average time/residue: 0.1301 time to fit residues: 66.7543 Evaluate side-chains 361 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 127 optimal weight: 0.0670 chunk 134 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** 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 = 0.4219 r_free = 0.4219 target = 0.177203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139983 restraints weight = 25210.533| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.43 r_work: 0.3597 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14994 Z= 0.175 Angle : 0.601 9.260 20468 Z= 0.315 Chirality : 0.042 0.187 2341 Planarity : 0.004 0.052 2407 Dihedral : 17.602 87.392 2445 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.90 % Allowed : 27.62 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1661 helix: 1.26 (0.18), residues: 817 sheet: -0.77 (0.35), residues: 226 loop : -0.95 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 938 TYR 0.014 0.001 TYR A 656 PHE 0.019 0.002 PHE A 447 TRP 0.008 0.001 TRP B 807 HIS 0.008 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (14994) covalent geometry : angle 0.60114 / 0.31 (20468) hydrogen bonds : bond 0.03925 / 2.54 ( 774) hydrogen bonds : angle 4.39718 / 3.11 ( 2143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 81 SER cc_start: 0.8626 (p) cc_final: 0.8370 (t) REVERT: A 229 LYS cc_start: 0.8330 (mppt) cc_final: 0.8110 (mppt) REVERT: A 274 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (tp) REVERT: A 371 GLU cc_start: 0.7272 (pm20) cc_final: 0.6877 (mp0) REVERT: A 701 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: B 544 ASN cc_start: 0.7797 (m-40) cc_final: 0.7516 (m-40) REVERT: B 677 GLU cc_start: 0.7677 (tp30) cc_final: 0.7410 (tp30) REVERT: B 854 GLU cc_start: 0.7842 (pm20) cc_final: 0.7336 (mp0) REVERT: B 889 GLU cc_start: 0.7285 (pt0) cc_final: 0.6999 (pt0) REVERT: B 918 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7507 (pt) REVERT: B 955 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: B 961 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 968 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8432 (t) REVERT: B 979 ARG cc_start: 0.6931 (ptp-110) cc_final: 0.6621 (ptp-110) outliers start: 57 outliers final: 45 residues processed: 362 average time/residue: 0.1283 time to fit residues: 67.5384 Evaluate side-chains 371 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 155 optimal weight: 0.0470 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 109 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.177496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140265 restraints weight = 25256.885| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.44 r_work: 0.3601 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14994 Z= 0.152 Angle : 0.617 9.216 20468 Z= 0.320 Chirality : 0.041 0.188 2341 Planarity : 0.004 0.051 2407 Dihedral : 17.580 83.654 2445 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.63 % Allowed : 28.76 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1661 helix: 1.29 (0.18), residues: 816 sheet: -0.77 (0.35), residues: 226 loop : -0.98 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 752 TYR 0.011 0.001 TYR A 408 PHE 0.022 0.002 PHE A 760 TRP 0.009 0.001 TRP A 764 HIS 0.008 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14994) covalent geometry : angle 0.61669 / 0.32 (20468) hydrogen bonds : bond 0.03845 / 2.49 ( 774) hydrogen bonds : angle 4.37646 / 3.09 ( 2143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 81 SER cc_start: 0.8626 (p) cc_final: 0.8372 (t) REVERT: A 171 ARG cc_start: 0.6485 (mtt90) cc_final: 0.5912 (mtt90) REVERT: A 229 LYS cc_start: 0.8318 (mppt) cc_final: 0.8107 (mppt) REVERT: A 274 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (tp) REVERT: A 303 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: A 371 GLU cc_start: 0.7276 (pm20) cc_final: 0.6873 (mp0) REVERT: A 701 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: B 269 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6658 (mm-30) REVERT: B 544 ASN cc_start: 0.7784 (m-40) cc_final: 0.7550 (m110) REVERT: B 677 GLU cc_start: 0.7641 (tp30) cc_final: 0.7373 (tp30) REVERT: B 854 GLU cc_start: 0.7807 (pm20) cc_final: 0.7314 (mp0) REVERT: B 889 GLU cc_start: 0.7265 (pt0) cc_final: 0.7002 (pt0) REVERT: B 918 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7512 (pt) REVERT: B 955 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: B 968 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8380 (t) REVERT: B 979 ARG cc_start: 0.6923 (ptp-110) cc_final: 0.6576 (ptp-110) outliers start: 53 outliers final: 43 residues processed: 360 average time/residue: 0.1306 time to fit residues: 68.0416 Evaluate side-chains 364 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 955 GLU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 58 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.178558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140546 restraints weight = 28785.567| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.66 r_work: 0.3595 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14994 Z= 0.129 Angle : 0.615 9.840 20468 Z= 0.320 Chirality : 0.041 0.194 2341 Planarity : 0.004 0.057 2407 Dihedral : 17.543 77.516 2445 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.49 % Allowed : 29.10 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1661 helix: 1.36 (0.18), residues: 816 sheet: -0.77 (0.35), residues: 228 loop : -1.00 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 616 TYR 0.014 0.001 TYR A 408 PHE 0.028 0.001 PHE A 384 TRP 0.008 0.001 TRP A 764 HIS 0.007 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (14994) covalent geometry : angle 0.61504 / 0.32 (20468) hydrogen bonds : bond 0.03730 / 2.42 ( 774) hydrogen bonds : angle 4.33196 / 3.07 ( 2143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8292 (p) REVERT: A 81 SER cc_start: 0.8637 (p) cc_final: 0.8397 (t) REVERT: A 171 ARG cc_start: 0.6441 (mtt90) cc_final: 0.6033 (mtt90) REVERT: A 188 GLU cc_start: 0.7963 (tp30) cc_final: 0.7628 (tp30) REVERT: A 274 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6958 (tp) REVERT: A 371 GLU cc_start: 0.7308 (pm20) cc_final: 0.6882 (mp0) REVERT: A 376 LEU cc_start: 0.8201 (mt) cc_final: 0.7874 (mp) REVERT: A 501 ARG cc_start: 0.3065 (OUTLIER) cc_final: 0.2490 (ptm-80) REVERT: A 680 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7375 (mtt180) REVERT: A 701 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: A 918 LYS cc_start: 0.7193 (tptp) cc_final: 0.6939 (tptp) REVERT: B 269 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6653 (mm-30) REVERT: B 544 ASN cc_start: 0.7739 (m-40) cc_final: 0.7449 (m-40) REVERT: B 677 GLU cc_start: 0.7607 (tp30) cc_final: 0.7343 (tp30) REVERT: B 854 GLU cc_start: 0.7779 (pm20) cc_final: 0.7307 (mp0) REVERT: B 889 GLU cc_start: 0.7311 (pt0) cc_final: 0.7039 (pt0) REVERT: B 920 SER cc_start: 0.8385 (p) cc_final: 0.8095 (p) REVERT: B 968 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8368 (t) REVERT: B 979 ARG cc_start: 0.6920 (ptp-110) cc_final: 0.6570 (ptp-110) outliers start: 51 outliers final: 41 residues processed: 353 average time/residue: 0.1347 time to fit residues: 69.0426 Evaluate side-chains 359 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 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 = 0.4238 r_free = 0.4238 target = 0.179796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142907 restraints weight = 22429.282| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.29 r_work: 0.3630 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14994 Z= 0.143 Angle : 0.630 11.226 20468 Z= 0.325 Chirality : 0.041 0.196 2341 Planarity : 0.004 0.077 2407 Dihedral : 17.518 77.352 2444 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.43 % Allowed : 29.03 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1661 helix: 1.35 (0.18), residues: 816 sheet: -0.75 (0.34), residues: 227 loop : -1.03 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 616 TYR 0.012 0.001 TYR A 408 PHE 0.022 0.001 PHE A 384 TRP 0.009 0.001 TRP A 764 HIS 0.014 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14994) covalent geometry : angle 0.62980 / 0.33 (20468) hydrogen bonds : bond 0.03759 / 2.43 ( 774) hydrogen bonds : angle 4.33497 / 3.07 ( 2143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6414 (mtt90) cc_final: 0.5958 (mtt90) REVERT: A 274 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 371 GLU cc_start: 0.7230 (pm20) cc_final: 0.6820 (mp0) REVERT: A 376 LEU cc_start: 0.8189 (mt) cc_final: 0.7845 (mp) REVERT: A 501 ARG cc_start: 0.3044 (OUTLIER) cc_final: 0.2460 (ptm-80) REVERT: A 569 GLU cc_start: 0.7281 (mp0) cc_final: 0.7027 (mp0) REVERT: A 680 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7333 (mtt180) REVERT: A 701 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: A 918 LYS cc_start: 0.7182 (tptp) cc_final: 0.6938 (tptp) REVERT: B 269 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 544 ASN cc_start: 0.7694 (m-40) cc_final: 0.7397 (m-40) REVERT: B 677 GLU cc_start: 0.7591 (tp30) cc_final: 0.7312 (tp30) REVERT: B 714 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7637 (ptpt) REVERT: B 854 GLU cc_start: 0.7756 (pm20) cc_final: 0.7294 (mp0) REVERT: B 889 GLU cc_start: 0.7203 (pt0) cc_final: 0.6938 (pt0) REVERT: B 920 SER cc_start: 0.8372 (p) cc_final: 0.8090 (p) REVERT: B 979 ARG cc_start: 0.6883 (ptp-110) cc_final: 0.6509 (ptp-110) outliers start: 50 outliers final: 40 residues processed: 349 average time/residue: 0.1328 time to fit residues: 66.9971 Evaluate side-chains 355 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 5 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 159 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 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 = 0.4225 r_free = 0.4225 target = 0.177690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141058 restraints weight = 22363.596| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.25 r_work: 0.3629 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14994 Z= 0.169 Angle : 0.639 10.613 20468 Z= 0.330 Chirality : 0.042 0.213 2341 Planarity : 0.005 0.143 2407 Dihedral : 17.524 77.397 2444 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.16 % Allowed : 29.64 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1661 helix: 1.27 (0.18), residues: 817 sheet: -0.73 (0.35), residues: 226 loop : -1.06 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 711 TYR 0.010 0.001 TYR A 121 PHE 0.021 0.002 PHE A 760 TRP 0.008 0.001 TRP A 764 HIS 0.018 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14994) covalent geometry : angle 0.63863 / 0.33 (20468) hydrogen bonds : bond 0.03839 / 2.49 ( 774) hydrogen bonds : angle 4.37370 / 3.10 ( 2143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4216.97 seconds wall clock time: 73 minutes 3.38 seconds (4383.38 seconds total)