Starting phenix.real_space_refine on Thu Mar 5 01:02:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.map" model { file = "/net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v9y_21130/03_2026/6v9y_21130.cif" } resolution = 3.6 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= 1.000 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 11628 2.51 5 N 2952 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17716 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4429 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 80 Restraints were copied for chains: B, D, C Time building chain proxies: 3.47, per 1000 atoms: 0.20 Number of scatterers: 17716 At special positions: 0 Unit cell: (110.62, 109.404, 138.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3012 8.00 N 2952 7.00 C 11628 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: 1.44 Conformation dependent library (CDL) restraints added in 822.3 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 71.8% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP A 515 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.546A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU A 625 " --> pdb=" O CYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.639A pdb=" N MET A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 720 " --> pdb=" O PHE A 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Proline residue: A 732 - end of helix removed outlier: 3.683A pdb=" N ASN A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 778 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 827 through 850 removed outlier: 3.504A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE A 898 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 3.742A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS A 997 " --> pdb=" O TRP A 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 998 " --> pdb=" O PHE A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A1069 " --> pdb=" O ILE A1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP B 515 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL B 532 " --> pdb=" O GLN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.545A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU B 625 " --> pdb=" O CYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.638A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU B 698 " --> pdb=" O ARG B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 714 Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS B 719 " --> pdb=" O GLY B 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 720 " --> pdb=" O PHE B 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 724 " --> pdb=" O MET B 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 725 " --> pdb=" O MET B 721 " (cutoff:3.500A) Proline residue: B 732 - end of helix removed outlier: 3.683A pdb=" N ASN B 739 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 778 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 782 " --> pdb=" O PHE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE B 816 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 823 Processing helix chain 'B' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL B 861 " --> pdb=" O GLY B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 892 removed outlier: 5.531A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE B 898 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.742A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 988 " --> pdb=" O THR B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 4.105A pdb=" N LYS B 997 " --> pdb=" O TRP B 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 998 " --> pdb=" O PHE B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 3.543A pdb=" N LYS B1060 " --> pdb=" O PHE B1056 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP D 515 " --> pdb=" O HIS D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.643A pdb=" N HIS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL D 532 " --> pdb=" O GLN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.545A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 569 Processing helix chain 'D' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 611 Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU D 625 " --> pdb=" O CYS D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.638A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 699 removed outlier: 3.513A pdb=" N LEU D 698 " --> pdb=" O ARG D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 714 Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS D 719 " --> pdb=" O GLY D 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 720 " --> pdb=" O PHE D 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 725 " --> pdb=" O MET D 721 " (cutoff:3.500A) Proline residue: D 732 - end of helix removed outlier: 3.684A pdb=" N ASN D 739 " --> pdb=" O ILE D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 778 " --> pdb=" O MET D 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 782 " --> pdb=" O PHE D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE D 816 " --> pdb=" O TYR D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 823 Processing helix chain 'D' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 853 No H-bonds generated for 'chain 'D' and resid 851 through 853' Processing helix chain 'D' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.687A pdb=" N PHE D 898 " --> pdb=" O GLN D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 911 Processing helix chain 'D' and resid 922 through 927 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 3.743A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 988 " --> pdb=" O THR D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS D 997 " --> pdb=" O TRP D 993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 998 " --> pdb=" O PHE D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS D1060 " --> pdb=" O PHE D1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D1069 " --> pdb=" O ILE D1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.574A pdb=" N LEU C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP C 515 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.507A pdb=" N VAL C 532 " --> pdb=" O GLN C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.546A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 Processing helix chain 'C' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 611 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.598A pdb=" N GLU C 625 " --> pdb=" O CYS C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.639A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.800A pdb=" N MET C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU C 698 " --> pdb=" O ARG C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.638A pdb=" N HIS C 719 " --> pdb=" O GLY C 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 720 " --> pdb=" O PHE C 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 725 " --> pdb=" O MET C 721 " (cutoff:3.500A) Proline residue: C 732 - end of helix removed outlier: 3.683A pdb=" N ASN C 739 " --> pdb=" O ILE C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL C 777 " --> pdb=" O CYS C 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 778 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 782 " --> pdb=" O PHE C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 819 removed outlier: 3.691A pdb=" N ILE C 816 " --> pdb=" O TYR C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 823 Processing helix chain 'C' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE C 898 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 911 Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 968 removed outlier: 3.586A pdb=" N ALA C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 3.743A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 988 " --> pdb=" O THR C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS C 997 " --> pdb=" O TRP C 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 998 " --> pdb=" O PHE C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS C1060 " --> pdb=" O PHE C1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C1069 " --> pdb=" O ILE C1065 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR A 655 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1003 " --> pdb=" O TYR A 658 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR B 655 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B1003 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR D 655 " --> pdb=" O SER D 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D1003 " --> pdb=" O TYR D 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR C 655 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C1003 " --> pdb=" O TYR C 658 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.95 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: 5462 1.34 - 1.46: 3982 1.46 - 1.58: 8444 1.58 - 1.70: 4 1.70 - 1.82: 204 Bond restraints: 18096 Sorted by residual: bond pdb=" C LEU A 820 " pdb=" N PRO A 821 " ideal model delta sigma weight residual 1.337 1.369 -0.033 9.80e-03 1.04e+04 1.12e+01 bond pdb=" C LEU D 820 " pdb=" N PRO D 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.10e+01 bond pdb=" C LEU C 820 " pdb=" N PRO C 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.09e+01 bond pdb=" C LEU B 820 " pdb=" N PRO B 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.08e+01 bond pdb=" CB VAL C 948 " pdb=" CG2 VAL C 948 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.74e+00 ... (remaining 18091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 24019 3.43 - 6.85: 430 6.85 - 10.28: 47 10.28 - 13.70: 16 13.70 - 17.13: 8 Bond angle restraints: 24520 Sorted by residual: angle pdb=" CG LYS C 503 " pdb=" CD LYS C 503 " pdb=" CE LYS C 503 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 angle pdb=" CG LYS A 503 " pdb=" CD LYS A 503 " pdb=" CE LYS A 503 " ideal model delta sigma weight residual 111.30 123.81 -12.51 2.30e+00 1.89e-01 2.96e+01 angle pdb=" CG LYS D 503 " pdb=" CD LYS D 503 " pdb=" CE LYS D 503 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CG LYS B 503 " pdb=" CD LYS B 503 " pdb=" CE LYS B 503 " ideal model delta sigma weight residual 111.30 123.79 -12.49 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CD LYS B 503 " pdb=" CE LYS B 503 " pdb=" NZ LYS B 503 " ideal model delta sigma weight residual 111.90 128.42 -16.52 3.20e+00 9.77e-02 2.67e+01 ... (remaining 24515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 9605 15.97 - 31.94: 911 31.94 - 47.92: 232 47.92 - 63.89: 52 63.89 - 79.86: 16 Dihedral angle restraints: 10816 sinusoidal: 4204 harmonic: 6612 Sorted by residual: dihedral pdb=" CA LEU C 576 " pdb=" C LEU C 576 " pdb=" N ASN C 577 " pdb=" CA ASN C 577 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LEU A 576 " pdb=" C LEU A 576 " pdb=" N ASN A 577 " pdb=" CA ASN A 577 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU D 576 " pdb=" C LEU D 576 " pdb=" N ASN D 577 " pdb=" CA ASN D 577 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 10813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2601 0.098 - 0.195: 280 0.195 - 0.293: 11 0.293 - 0.391: 4 0.391 - 0.489: 4 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CB ILE C 811 " pdb=" CA ILE C 811 " pdb=" CG1 ILE C 811 " pdb=" CG2 ILE C 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CB ILE D 811 " pdb=" CA ILE D 811 " pdb=" CG1 ILE D 811 " pdb=" CG2 ILE D 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 2897 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 821 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO A 821 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 820 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO D 821 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 821 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 821 " -0.046 5.00e-02 4.00e+02 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4863 2.79 - 3.32: 16694 3.32 - 3.84: 28789 3.84 - 4.37: 34410 4.37 - 4.90: 55778 Nonbonded interactions: 140534 Sorted by model distance: nonbonded pdb=" NH1 ARG D 458 " pdb=" O MET C1072 " model vdw 2.262 3.120 nonbonded pdb=" OG1 THR D 814 " pdb=" O CYS D 834 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR B 814 " pdb=" O CYS B 834 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR A 814 " pdb=" O CYS A 834 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR C 814 " pdb=" O CYS C 834 " model vdw 2.319 3.040 ... (remaining 140529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.650 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 18096 Z= 0.403 Angle : 1.182 17.130 24520 Z= 0.590 Chirality : 0.065 0.489 2900 Planarity : 0.008 0.083 3008 Dihedral : 14.212 79.858 6512 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.13 % Allowed : 10.02 % Favored : 87.85 % 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: -5.18 (0.13), residues: 2208 helix: -3.75 (0.07), residues: 1460 sheet: 1.08 (0.73), residues: 60 loop : -2.57 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 852 TYR 0.024 0.003 TYR C 842 PHE 0.017 0.002 PHE A 944 TRP 0.018 0.003 TRP B 605 HIS 0.011 0.002 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00909 (18096) covalent geometry : angle 1.18239 (24520) hydrogen bonds : bond 0.27797 ( 958) hydrogen bonds : angle 9.58870 ( 2838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 474 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.9391 (mt) cc_final: 0.9152 (pp) REVERT: A 491 LYS cc_start: 0.9395 (tttt) cc_final: 0.9143 (ttmm) REVERT: A 502 LEU cc_start: 0.9706 (mm) cc_final: 0.9492 (mm) REVERT: A 509 LEU cc_start: 0.9000 (mm) cc_final: 0.8763 (mm) REVERT: A 634 MET cc_start: 0.9464 (tpt) cc_final: 0.9178 (tpt) REVERT: A 704 LYS cc_start: 0.9530 (mttt) cc_final: 0.9299 (mtmm) REVERT: A 721 MET cc_start: 0.8372 (mmm) cc_final: 0.7958 (tmm) REVERT: A 808 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8544 (mt-10) REVERT: A 834 CYS cc_start: 0.9015 (m) cc_final: 0.8743 (m) REVERT: A 840 TYR cc_start: 0.9142 (t80) cc_final: 0.8868 (t80) REVERT: A 845 ASN cc_start: 0.8777 (t0) cc_final: 0.8469 (t0) REVERT: A 978 MET cc_start: 0.8118 (ttp) cc_final: 0.7183 (ttm) REVERT: A 1053 ASP cc_start: 0.8481 (t70) cc_final: 0.8169 (t0) REVERT: A 1071 LYS cc_start: 0.9325 (mttm) cc_final: 0.8939 (mmmm) REVERT: B 491 LYS cc_start: 0.9394 (tttt) cc_final: 0.9121 (ttpp) REVERT: B 509 LEU cc_start: 0.9035 (mm) cc_final: 0.8789 (mm) REVERT: B 522 SER cc_start: 0.9343 (m) cc_final: 0.9114 (p) REVERT: B 635 LYS cc_start: 0.9481 (tttt) cc_final: 0.9262 (ttmt) REVERT: B 721 MET cc_start: 0.8176 (mmm) cc_final: 0.7954 (tmm) REVERT: B 834 CYS cc_start: 0.9010 (m) cc_final: 0.8652 (m) REVERT: B 845 ASN cc_start: 0.8887 (t0) cc_final: 0.7882 (t0) REVERT: B 849 TYR cc_start: 0.8990 (m-80) cc_final: 0.8720 (m-10) REVERT: B 1045 LEU cc_start: 0.9439 (tp) cc_final: 0.9133 (tt) REVERT: B 1053 ASP cc_start: 0.8207 (t70) cc_final: 0.7957 (t70) REVERT: B 1059 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 1071 LYS cc_start: 0.9257 (mttm) cc_final: 0.9041 (mmmm) REVERT: B 1072 MET cc_start: 0.7499 (ttp) cc_final: 0.7202 (tmm) REVERT: D 464 ARG cc_start: 0.9184 (mtm110) cc_final: 0.8948 (mtm110) REVERT: D 491 LYS cc_start: 0.9434 (tttt) cc_final: 0.9142 (ttpp) REVERT: D 522 SER cc_start: 0.9490 (m) cc_final: 0.9246 (p) REVERT: D 634 MET cc_start: 0.9431 (tpt) cc_final: 0.8955 (tpp) REVERT: D 704 LYS cc_start: 0.9402 (mttt) cc_final: 0.9081 (mttm) REVERT: D 721 MET cc_start: 0.8184 (mmm) cc_final: 0.7682 (tmm) REVERT: D 834 CYS cc_start: 0.8814 (m) cc_final: 0.8613 (m) REVERT: D 844 MET cc_start: 0.9217 (mmt) cc_final: 0.8675 (tpp) REVERT: D 845 ASN cc_start: 0.8760 (t0) cc_final: 0.8521 (t0) REVERT: D 862 MET cc_start: 0.8861 (mtt) cc_final: 0.8649 (mtt) REVERT: D 1053 ASP cc_start: 0.8140 (t70) cc_final: 0.7928 (t70) REVERT: D 1059 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8100 (mm-30) REVERT: C 459 ILE cc_start: 0.9437 (mm) cc_final: 0.9216 (tt) REVERT: C 491 LYS cc_start: 0.9376 (tttt) cc_final: 0.9124 (ttpp) REVERT: C 522 SER cc_start: 0.9535 (m) cc_final: 0.9195 (p) REVERT: C 544 LEU cc_start: 0.9174 (mt) cc_final: 0.8928 (tp) REVERT: C 635 LYS cc_start: 0.9539 (tttt) cc_final: 0.9264 (ttmt) REVERT: C 834 CYS cc_start: 0.8964 (m) cc_final: 0.8643 (m) REVERT: C 845 ASN cc_start: 0.8741 (t0) cc_final: 0.8317 (t0) REVERT: C 1045 LEU cc_start: 0.9378 (tp) cc_final: 0.8966 (tt) REVERT: C 1053 ASP cc_start: 0.8308 (t70) cc_final: 0.8065 (t70) REVERT: C 1059 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8246 (mm-30) outliers start: 40 outliers final: 12 residues processed: 496 average time/residue: 0.1207 time to fit residues: 93.3578 Evaluate side-chains 351 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 339 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 644 HIS A 700 HIS A 831 GLN A 954 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 644 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS B 829 HIS B 831 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS D 537 ASN D 644 HIS D 700 HIS D 719 HIS D 831 GLN ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN C 519 HIS C 644 HIS C 700 HIS C 829 HIS C 831 GLN C 907 GLN C 933 HIS C 954 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075444 restraints weight = 50077.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078041 restraints weight = 25674.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.079748 restraints weight = 16742.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080821 restraints weight = 12683.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081618 restraints weight = 10604.293| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18096 Z= 0.152 Angle : 0.715 11.547 24520 Z= 0.357 Chirality : 0.044 0.272 2900 Planarity : 0.006 0.059 3008 Dihedral : 6.328 51.940 2402 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.37 % Allowed : 15.30 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.69 (0.15), residues: 2208 helix: -1.53 (0.11), residues: 1584 sheet: 3.74 (0.73), residues: 40 loop : -2.42 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 473 TYR 0.014 0.001 TYR C 456 PHE 0.016 0.001 PHE A 583 TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS D 589 Details of bonding type rmsd covalent geometry : bond 0.00342 (18096) covalent geometry : angle 0.71512 (24520) hydrogen bonds : bond 0.04812 ( 958) hydrogen bonds : angle 4.80238 ( 2838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 427 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.9438 (tttt) cc_final: 0.9076 (ptmm) REVERT: A 509 LEU cc_start: 0.9148 (mm) cc_final: 0.8859 (mm) REVERT: A 586 LEU cc_start: 0.9562 (tp) cc_final: 0.9145 (tp) REVERT: A 721 MET cc_start: 0.8577 (mmm) cc_final: 0.7845 (tmm) REVERT: A 776 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9115 (tt) REVERT: A 834 CYS cc_start: 0.9138 (m) cc_final: 0.8846 (m) REVERT: A 982 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9097 (tp) REVERT: A 1045 LEU cc_start: 0.9367 (tp) cc_final: 0.9062 (tt) REVERT: A 1053 ASP cc_start: 0.8921 (t70) cc_final: 0.8551 (t70) REVERT: A 1066 LYS cc_start: 0.9233 (mttt) cc_final: 0.8997 (mtpt) REVERT: A 1071 LYS cc_start: 0.9363 (mttm) cc_final: 0.9054 (mmmm) REVERT: A 1072 MET cc_start: 0.7538 (tmm) cc_final: 0.7248 (tmm) REVERT: B 463 GLN cc_start: 0.9160 (mt0) cc_final: 0.8894 (mt0) REVERT: B 491 LYS cc_start: 0.9376 (tttt) cc_final: 0.9069 (ptmm) REVERT: B 509 LEU cc_start: 0.9009 (mm) cc_final: 0.8730 (mm) REVERT: B 544 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 586 LEU cc_start: 0.9542 (tp) cc_final: 0.9303 (tp) REVERT: B 635 LYS cc_start: 0.9333 (tttt) cc_final: 0.9095 (ttmt) REVERT: B 709 MET cc_start: 0.8578 (tmm) cc_final: 0.8287 (tmm) REVERT: B 720 MET cc_start: 0.8578 (mmp) cc_final: 0.8024 (mmm) REVERT: B 721 MET cc_start: 0.8325 (mmm) cc_final: 0.8041 (tmm) REVERT: B 776 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9282 (tp) REVERT: B 834 CYS cc_start: 0.9003 (m) cc_final: 0.8684 (m) REVERT: B 840 TYR cc_start: 0.9122 (t80) cc_final: 0.8892 (t80) REVERT: B 845 ASN cc_start: 0.8631 (t0) cc_final: 0.8117 (t0) REVERT: B 1045 LEU cc_start: 0.9313 (tp) cc_final: 0.9090 (tt) REVERT: B 1053 ASP cc_start: 0.8772 (t70) cc_final: 0.8497 (t70) REVERT: B 1056 PHE cc_start: 0.8944 (t80) cc_final: 0.8689 (t80) REVERT: B 1059 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 1066 LYS cc_start: 0.9352 (mttt) cc_final: 0.9066 (mtpt) REVERT: D 491 LYS cc_start: 0.9509 (tttt) cc_final: 0.9082 (ttpp) REVERT: D 522 SER cc_start: 0.9567 (m) cc_final: 0.9106 (p) REVERT: D 623 ILE cc_start: 0.8979 (tt) cc_final: 0.8723 (tp) REVERT: D 626 MET cc_start: 0.9312 (ttp) cc_final: 0.8999 (ttm) REVERT: D 634 MET cc_start: 0.9593 (tpt) cc_final: 0.9211 (tpt) REVERT: D 686 LEU cc_start: 0.9324 (tp) cc_final: 0.9102 (tp) REVERT: D 704 LYS cc_start: 0.9497 (mttt) cc_final: 0.9206 (mttm) REVERT: D 721 MET cc_start: 0.8300 (mmm) cc_final: 0.7644 (tmt) REVERT: D 803 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7532 (tp) REVERT: D 834 CYS cc_start: 0.9056 (m) cc_final: 0.8808 (m) REVERT: D 844 MET cc_start: 0.9359 (mmt) cc_final: 0.8705 (tpp) REVERT: D 845 ASN cc_start: 0.9042 (t0) cc_final: 0.8776 (t0) REVERT: D 891 LEU cc_start: 0.9483 (mt) cc_final: 0.8980 (mt) REVERT: D 941 LEU cc_start: 0.9351 (tp) cc_final: 0.9144 (tp) REVERT: D 1041 GLU cc_start: 0.8849 (tt0) cc_final: 0.8525 (mp0) REVERT: D 1053 ASP cc_start: 0.8665 (t70) cc_final: 0.8363 (t70) REVERT: D 1060 LYS cc_start: 0.9278 (mtmm) cc_final: 0.8715 (ptpp) REVERT: D 1063 GLU cc_start: 0.8993 (tp30) cc_final: 0.8720 (tp30) REVERT: C 466 LEU cc_start: 0.9554 (mt) cc_final: 0.9347 (mt) REVERT: C 491 LYS cc_start: 0.9400 (tttt) cc_final: 0.9088 (ptmm) REVERT: C 544 LEU cc_start: 0.9307 (mt) cc_final: 0.9027 (mt) REVERT: C 720 MET cc_start: 0.8150 (mmm) cc_final: 0.7938 (mmm) REVERT: C 721 MET cc_start: 0.7963 (tmm) cc_final: 0.7386 (tmm) REVERT: C 727 CYS cc_start: 0.9340 (t) cc_final: 0.9044 (t) REVERT: C 776 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9114 (tp) REVERT: C 816 ILE cc_start: 0.9494 (pt) cc_final: 0.9241 (pt) REVERT: C 834 CYS cc_start: 0.9265 (m) cc_final: 0.8991 (m) REVERT: C 840 TYR cc_start: 0.9416 (t80) cc_final: 0.9145 (t80) REVERT: C 848 LEU cc_start: 0.9358 (mp) cc_final: 0.9070 (tp) REVERT: C 1045 LEU cc_start: 0.9422 (tp) cc_final: 0.9141 (tt) REVERT: C 1053 ASP cc_start: 0.8830 (t70) cc_final: 0.8584 (t70) REVERT: C 1059 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 82 outliers final: 43 residues processed: 476 average time/residue: 0.1135 time to fit residues: 86.1999 Evaluate side-chains 400 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 1068 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 154 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 222 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 HIS A 907 GLN A 933 HIS B 467 GLN B 907 GLN B 933 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN D 499 GLN D 907 GLN D 940 GLN ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076236 restraints weight = 50819.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078835 restraints weight = 25487.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080584 restraints weight = 16380.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081645 restraints weight = 12277.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082197 restraints weight = 10213.568| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18096 Z= 0.125 Angle : 0.650 10.352 24520 Z= 0.323 Chirality : 0.043 0.214 2900 Planarity : 0.004 0.055 3008 Dihedral : 5.515 57.749 2389 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.00 % Allowed : 18.34 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2208 helix: -0.37 (0.12), residues: 1576 sheet: 3.90 (0.75), residues: 40 loop : -2.24 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 473 TYR 0.016 0.001 TYR A 840 PHE 0.027 0.001 PHE D 944 TRP 0.012 0.001 TRP A 711 HIS 0.002 0.001 HIS D 719 Details of bonding type rmsd covalent geometry : bond 0.00284 (18096) covalent geometry : angle 0.65010 (24520) hydrogen bonds : bond 0.03948 ( 958) hydrogen bonds : angle 4.26691 ( 2838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 406 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.9453 (tttt) cc_final: 0.9130 (ptmm) REVERT: A 509 LEU cc_start: 0.9114 (mm) cc_final: 0.8836 (mm) REVERT: A 544 LEU cc_start: 0.9396 (mt) cc_final: 0.9087 (mt) REVERT: A 586 LEU cc_start: 0.9592 (tp) cc_final: 0.9204 (tp) REVERT: A 704 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9334 (mttp) REVERT: A 721 MET cc_start: 0.8627 (mmm) cc_final: 0.7968 (tmm) REVERT: A 776 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9109 (tt) REVERT: A 808 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8461 (mp0) REVERT: A 834 CYS cc_start: 0.9103 (m) cc_final: 0.8853 (m) REVERT: A 840 TYR cc_start: 0.9116 (t80) cc_final: 0.8817 (t80) REVERT: A 842 TYR cc_start: 0.8959 (m-80) cc_final: 0.8173 (t80) REVERT: A 1045 LEU cc_start: 0.9370 (tp) cc_final: 0.9118 (tt) REVERT: A 1053 ASP cc_start: 0.8881 (t70) cc_final: 0.8498 (t0) REVERT: A 1056 PHE cc_start: 0.8967 (t80) cc_final: 0.8729 (t80) REVERT: A 1066 LYS cc_start: 0.9208 (mttt) cc_final: 0.9005 (mtpt) REVERT: A 1072 MET cc_start: 0.7651 (tmm) cc_final: 0.6904 (tmm) REVERT: B 466 LEU cc_start: 0.9615 (mt) cc_final: 0.9381 (mt) REVERT: B 491 LYS cc_start: 0.9302 (tttt) cc_final: 0.9032 (ptmm) REVERT: B 504 LYS cc_start: 0.9548 (mttt) cc_final: 0.9306 (mtmt) REVERT: B 509 LEU cc_start: 0.8993 (mm) cc_final: 0.8707 (mm) REVERT: B 544 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8878 (tp) REVERT: B 586 LEU cc_start: 0.9588 (tp) cc_final: 0.9374 (tp) REVERT: B 635 LYS cc_start: 0.9214 (tttt) cc_final: 0.8953 (ttmt) REVERT: B 720 MET cc_start: 0.8540 (mmp) cc_final: 0.8000 (mmm) REVERT: B 805 ASN cc_start: 0.8955 (m110) cc_final: 0.8530 (t0) REVERT: B 834 CYS cc_start: 0.8952 (m) cc_final: 0.8633 (m) REVERT: B 845 ASN cc_start: 0.8719 (t0) cc_final: 0.8083 (t0) REVERT: B 1053 ASP cc_start: 0.8750 (t70) cc_final: 0.8460 (t70) REVERT: B 1059 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 1066 LYS cc_start: 0.9393 (mttt) cc_final: 0.9132 (mtpt) REVERT: D 491 LYS cc_start: 0.9438 (tttt) cc_final: 0.9139 (ptmm) REVERT: D 522 SER cc_start: 0.9482 (m) cc_final: 0.9025 (p) REVERT: D 530 MET cc_start: 0.9177 (mtp) cc_final: 0.8852 (mtp) REVERT: D 586 LEU cc_start: 0.9606 (tp) cc_final: 0.9390 (tp) REVERT: D 626 MET cc_start: 0.9287 (ttp) cc_final: 0.8880 (ttp) REVERT: D 634 MET cc_start: 0.9557 (tpt) cc_final: 0.9231 (tpt) REVERT: D 704 LYS cc_start: 0.9528 (mttt) cc_final: 0.9236 (mttm) REVERT: D 721 MET cc_start: 0.8267 (mmm) cc_final: 0.7673 (tmm) REVERT: D 844 MET cc_start: 0.9374 (mmt) cc_final: 0.8658 (tpp) REVERT: D 845 ASN cc_start: 0.8917 (t0) cc_final: 0.8665 (t0) REVERT: D 941 LEU cc_start: 0.9351 (tp) cc_final: 0.9120 (tp) REVERT: D 1053 ASP cc_start: 0.8682 (t70) cc_final: 0.8386 (t70) REVERT: D 1059 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8436 (mm-30) REVERT: D 1060 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8643 (ptpp) REVERT: D 1063 GLU cc_start: 0.8989 (tp30) cc_final: 0.8700 (tp30) REVERT: D 1072 MET cc_start: 0.8133 (tmm) cc_final: 0.7675 (tmm) REVERT: C 491 LYS cc_start: 0.9356 (tttt) cc_final: 0.8996 (ptmm) REVERT: C 544 LEU cc_start: 0.9314 (mt) cc_final: 0.9042 (mt) REVERT: C 586 LEU cc_start: 0.9607 (tp) cc_final: 0.9338 (tp) REVERT: C 720 MET cc_start: 0.8123 (mmm) cc_final: 0.7846 (mmm) REVERT: C 721 MET cc_start: 0.8019 (tmm) cc_final: 0.7784 (ppp) REVERT: C 727 CYS cc_start: 0.9347 (t) cc_final: 0.9050 (t) REVERT: C 805 ASN cc_start: 0.9016 (m110) cc_final: 0.8677 (t0) REVERT: C 816 ILE cc_start: 0.9480 (pt) cc_final: 0.9249 (pt) REVERT: C 834 CYS cc_start: 0.9253 (m) cc_final: 0.9004 (m) REVERT: C 840 TYR cc_start: 0.9368 (t80) cc_final: 0.9088 (t80) REVERT: C 848 LEU cc_start: 0.9286 (mp) cc_final: 0.9086 (tp) REVERT: C 1053 ASP cc_start: 0.8822 (t70) cc_final: 0.8559 (t70) REVERT: C 1059 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 1072 MET cc_start: 0.7685 (tmm) cc_final: 0.7305 (tmm) outliers start: 75 outliers final: 37 residues processed: 452 average time/residue: 0.1101 time to fit residues: 80.3736 Evaluate side-chains 402 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 362 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 0.0170 chunk 177 optimal weight: 6.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN B 494 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 HIS D 829 HIS D 907 GLN D1061 GLN C 494 HIS ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078723 restraints weight = 49320.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081310 restraints weight = 24281.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083006 restraints weight = 15374.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084183 restraints weight = 11355.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085002 restraints weight = 9286.685| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18096 Z= 0.123 Angle : 0.665 10.882 24520 Z= 0.319 Chirality : 0.042 0.218 2900 Planarity : 0.004 0.052 3008 Dihedral : 5.160 56.256 2387 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.32 % Allowed : 20.31 % Favored : 75.37 % 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: -0.60 (0.18), residues: 2208 helix: 0.15 (0.13), residues: 1576 sheet: 4.03 (0.74), residues: 40 loop : -2.03 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 473 TYR 0.011 0.001 TYR B 842 PHE 0.025 0.001 PHE D 944 TRP 0.009 0.001 TRP A 711 HIS 0.003 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00281 (18096) covalent geometry : angle 0.66540 (24520) hydrogen bonds : bond 0.03558 ( 958) hydrogen bonds : angle 4.12358 ( 2838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 386 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.9269 (mmm) cc_final: 0.8826 (mmp) REVERT: A 491 LYS cc_start: 0.9433 (tttt) cc_final: 0.9122 (ptmm) REVERT: A 509 LEU cc_start: 0.9045 (mm) cc_final: 0.8765 (mm) REVERT: A 544 LEU cc_start: 0.9378 (mt) cc_final: 0.9084 (mt) REVERT: A 586 LEU cc_start: 0.9630 (tp) cc_final: 0.9262 (tp) REVERT: A 642 MET cc_start: 0.8846 (mtp) cc_final: 0.8517 (mtt) REVERT: A 704 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9331 (mttp) REVERT: A 721 MET cc_start: 0.8532 (mmm) cc_final: 0.7942 (tmm) REVERT: A 803 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7741 (tp) REVERT: A 808 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8569 (mm-30) REVERT: A 834 CYS cc_start: 0.9053 (m) cc_final: 0.8834 (m) REVERT: A 840 TYR cc_start: 0.9162 (t80) cc_final: 0.8845 (t80) REVERT: A 842 TYR cc_start: 0.8982 (m-80) cc_final: 0.8192 (t80) REVERT: A 1045 LEU cc_start: 0.9398 (tp) cc_final: 0.9012 (tt) REVERT: A 1053 ASP cc_start: 0.8817 (t70) cc_final: 0.8419 (t0) REVERT: A 1056 PHE cc_start: 0.8987 (t80) cc_final: 0.8715 (t80) REVERT: A 1066 LYS cc_start: 0.9255 (mttt) cc_final: 0.9028 (mtpt) REVERT: A 1072 MET cc_start: 0.7725 (tmm) cc_final: 0.6916 (tmm) REVERT: B 491 LYS cc_start: 0.9287 (tttt) cc_final: 0.9022 (ptmm) REVERT: B 504 LYS cc_start: 0.9473 (mttt) cc_final: 0.9272 (mtmt) REVERT: B 509 LEU cc_start: 0.9024 (mm) cc_final: 0.8763 (mm) REVERT: B 544 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8745 (tp) REVERT: B 635 LYS cc_start: 0.9224 (tttt) cc_final: 0.8935 (ttmt) REVERT: B 720 MET cc_start: 0.8503 (mmp) cc_final: 0.8014 (mmm) REVERT: B 805 ASN cc_start: 0.8953 (m110) cc_final: 0.8490 (t0) REVERT: B 834 CYS cc_start: 0.8950 (m) cc_final: 0.8660 (m) REVERT: B 1053 ASP cc_start: 0.8696 (t70) cc_final: 0.8448 (t70) REVERT: B 1059 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 1066 LYS cc_start: 0.9336 (mttt) cc_final: 0.9081 (mtpt) REVERT: D 491 LYS cc_start: 0.9406 (tttt) cc_final: 0.9133 (ptmm) REVERT: D 518 LEU cc_start: 0.9249 (mt) cc_final: 0.9032 (mt) REVERT: D 522 SER cc_start: 0.9470 (m) cc_final: 0.9043 (p) REVERT: D 586 LEU cc_start: 0.9651 (tp) cc_final: 0.9213 (tp) REVERT: D 704 LYS cc_start: 0.9555 (mttt) cc_final: 0.9277 (mttm) REVERT: D 721 MET cc_start: 0.8298 (mmm) cc_final: 0.7787 (tmt) REVERT: D 844 MET cc_start: 0.9352 (mmt) cc_final: 0.8730 (tpp) REVERT: D 845 ASN cc_start: 0.8922 (t0) cc_final: 0.8654 (t0) REVERT: D 941 LEU cc_start: 0.9350 (tp) cc_final: 0.9118 (tp) REVERT: D 1053 ASP cc_start: 0.8699 (t70) cc_final: 0.8404 (t70) REVERT: D 1059 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8428 (mm-30) REVERT: D 1072 MET cc_start: 0.7983 (tmm) cc_final: 0.7513 (tmm) REVERT: C 491 LYS cc_start: 0.9366 (tttt) cc_final: 0.9010 (ptmm) REVERT: C 544 LEU cc_start: 0.9296 (mt) cc_final: 0.9049 (mt) REVERT: C 586 LEU cc_start: 0.9663 (tp) cc_final: 0.9417 (tp) REVERT: C 625 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8599 (mm-30) REVERT: C 721 MET cc_start: 0.7926 (tmm) cc_final: 0.7691 (ppp) REVERT: C 727 CYS cc_start: 0.9298 (t) cc_final: 0.8977 (t) REVERT: C 803 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8158 (tp) REVERT: C 805 ASN cc_start: 0.8959 (m110) cc_final: 0.8633 (t0) REVERT: C 808 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: C 816 ILE cc_start: 0.9487 (pt) cc_final: 0.9237 (pt) REVERT: C 834 CYS cc_start: 0.9219 (m) cc_final: 0.9005 (m) REVERT: C 840 TYR cc_start: 0.9328 (t80) cc_final: 0.9058 (t80) REVERT: C 848 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9059 (tp) REVERT: C 1045 LEU cc_start: 0.9281 (tp) cc_final: 0.9048 (tt) REVERT: C 1053 ASP cc_start: 0.8797 (t70) cc_final: 0.8530 (t70) REVERT: C 1059 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 1072 MET cc_start: 0.7795 (tmm) cc_final: 0.7381 (tmm) outliers start: 81 outliers final: 45 residues processed: 432 average time/residue: 0.1117 time to fit residues: 77.7014 Evaluate side-chains 400 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 349 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 499 GLN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 940 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.099216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078030 restraints weight = 49043.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080425 restraints weight = 25099.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082063 restraints weight = 16449.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083085 restraints weight = 12337.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083858 restraints weight = 10237.416| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18096 Z= 0.134 Angle : 0.669 11.697 24520 Z= 0.322 Chirality : 0.043 0.199 2900 Planarity : 0.004 0.050 3008 Dihedral : 4.964 50.364 2387 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.42 % Allowed : 22.17 % Favored : 73.40 % 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: -0.29 (0.18), residues: 2208 helix: 0.37 (0.13), residues: 1580 sheet: 4.10 (0.73), residues: 40 loop : -1.92 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 919 TYR 0.014 0.001 TYR B 840 PHE 0.019 0.001 PHE D 944 TRP 0.026 0.001 TRP C 605 HIS 0.003 0.001 HIS D 933 Details of bonding type rmsd covalent geometry : bond 0.00312 (18096) covalent geometry : angle 0.66872 (24520) hydrogen bonds : bond 0.03413 ( 958) hydrogen bonds : angle 4.08825 ( 2838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 365 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.9284 (mmm) cc_final: 0.8819 (mmp) REVERT: A 491 LYS cc_start: 0.9443 (tttt) cc_final: 0.9140 (ptmm) REVERT: A 509 LEU cc_start: 0.9086 (mm) cc_final: 0.8799 (mm) REVERT: A 544 LEU cc_start: 0.9404 (mt) cc_final: 0.9093 (mt) REVERT: A 586 LEU cc_start: 0.9634 (tp) cc_final: 0.9281 (tp) REVERT: A 642 MET cc_start: 0.8855 (mtp) cc_final: 0.8554 (mtt) REVERT: A 704 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9325 (mttp) REVERT: A 721 MET cc_start: 0.8586 (mmm) cc_final: 0.7957 (tmm) REVERT: A 808 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8576 (mm-30) REVERT: A 834 CYS cc_start: 0.9087 (m) cc_final: 0.8853 (m) REVERT: A 840 TYR cc_start: 0.9190 (t80) cc_final: 0.8794 (t80) REVERT: A 842 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8240 (t80) REVERT: A 1045 LEU cc_start: 0.9349 (tp) cc_final: 0.8917 (tt) REVERT: A 1053 ASP cc_start: 0.8842 (t70) cc_final: 0.8446 (t0) REVERT: A 1056 PHE cc_start: 0.8949 (t80) cc_final: 0.8711 (t80) REVERT: A 1066 LYS cc_start: 0.9253 (mttt) cc_final: 0.9021 (mtpt) REVERT: A 1072 MET cc_start: 0.7921 (tmm) cc_final: 0.7024 (tmm) REVERT: B 491 LYS cc_start: 0.9314 (tttt) cc_final: 0.9051 (ptmm) REVERT: B 509 LEU cc_start: 0.9007 (mm) cc_final: 0.8722 (mm) REVERT: B 544 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8799 (tp) REVERT: B 635 LYS cc_start: 0.9231 (tttt) cc_final: 0.8939 (ttmt) REVERT: B 720 MET cc_start: 0.8585 (mmp) cc_final: 0.8080 (mmm) REVERT: B 805 ASN cc_start: 0.8979 (m110) cc_final: 0.8508 (t0) REVERT: B 834 CYS cc_start: 0.8999 (m) cc_final: 0.8688 (m) REVERT: B 1053 ASP cc_start: 0.8727 (t70) cc_final: 0.8479 (t70) REVERT: B 1059 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 1066 LYS cc_start: 0.9324 (mttt) cc_final: 0.9063 (mtpt) REVERT: B 1072 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6380 (ptp) REVERT: D 491 LYS cc_start: 0.9404 (tttt) cc_final: 0.9133 (ptmm) REVERT: D 518 LEU cc_start: 0.9275 (mt) cc_final: 0.9071 (mt) REVERT: D 704 LYS cc_start: 0.9559 (mttt) cc_final: 0.9297 (mttp) REVERT: D 721 MET cc_start: 0.8282 (mmm) cc_final: 0.7782 (tmt) REVERT: D 776 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9120 (tt) REVERT: D 803 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7812 (tp) REVERT: D 808 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8767 (mm-30) REVERT: D 844 MET cc_start: 0.9345 (mmt) cc_final: 0.8685 (tpp) REVERT: D 845 ASN cc_start: 0.8957 (t0) cc_final: 0.8119 (t0) REVERT: D 941 LEU cc_start: 0.9375 (tp) cc_final: 0.9118 (tp) REVERT: D 1053 ASP cc_start: 0.8715 (t70) cc_final: 0.8415 (t70) REVERT: D 1072 MET cc_start: 0.8049 (tmm) cc_final: 0.7605 (tmm) REVERT: C 491 LYS cc_start: 0.9364 (tttt) cc_final: 0.9105 (ptmm) REVERT: C 544 LEU cc_start: 0.9326 (mt) cc_final: 0.9093 (mt) REVERT: C 720 MET cc_start: 0.8490 (mmp) cc_final: 0.8220 (mmm) REVERT: C 721 MET cc_start: 0.8007 (tmm) cc_final: 0.7388 (tmm) REVERT: C 727 CYS cc_start: 0.9308 (t) cc_final: 0.9003 (t) REVERT: C 808 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: C 816 ILE cc_start: 0.9478 (pt) cc_final: 0.9236 (pt) REVERT: C 834 CYS cc_start: 0.9238 (m) cc_final: 0.9009 (m) REVERT: C 840 TYR cc_start: 0.9307 (t80) cc_final: 0.8983 (t80) REVERT: C 842 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: C 848 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9093 (tp) REVERT: C 1053 ASP cc_start: 0.8853 (t70) cc_final: 0.8606 (t70) REVERT: C 1072 MET cc_start: 0.7864 (tmm) cc_final: 0.7465 (tmm) outliers start: 83 outliers final: 50 residues processed: 411 average time/residue: 0.1067 time to fit residues: 71.0872 Evaluate side-chains 397 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 633 CYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 99 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS B 577 ASN B1047 GLN D 467 GLN D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078144 restraints weight = 48881.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080612 restraints weight = 25198.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082278 restraints weight = 16453.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083201 restraints weight = 12369.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084019 restraints weight = 10376.626| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18096 Z= 0.125 Angle : 0.678 14.014 24520 Z= 0.321 Chirality : 0.042 0.207 2900 Planarity : 0.004 0.049 3008 Dihedral : 4.805 45.352 2385 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.89 % Allowed : 24.57 % Favored : 71.54 % 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: -0.11 (0.18), residues: 2208 helix: 0.50 (0.13), residues: 1576 sheet: 4.28 (0.73), residues: 40 loop : -1.81 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 473 TYR 0.014 0.001 TYR B 840 PHE 0.021 0.001 PHE B 783 TRP 0.026 0.001 TRP C 605 HIS 0.003 0.000 HIS D 933 Details of bonding type rmsd covalent geometry : bond 0.00291 (18096) covalent geometry : angle 0.67834 (24520) hydrogen bonds : bond 0.03322 ( 958) hydrogen bonds : angle 4.01266 ( 2838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 373 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.9333 (mmm) cc_final: 0.8848 (mmp) REVERT: A 491 LYS cc_start: 0.9445 (tttt) cc_final: 0.9135 (ptmm) REVERT: A 509 LEU cc_start: 0.9064 (mm) cc_final: 0.8761 (mm) REVERT: A 544 LEU cc_start: 0.9442 (mt) cc_final: 0.9152 (mt) REVERT: A 586 LEU cc_start: 0.9641 (tp) cc_final: 0.9308 (tp) REVERT: A 642 MET cc_start: 0.8912 (mtp) cc_final: 0.8615 (mtt) REVERT: A 704 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9307 (mttp) REVERT: A 721 MET cc_start: 0.8634 (mmm) cc_final: 0.7974 (tmm) REVERT: A 808 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8569 (mm-30) REVERT: A 834 CYS cc_start: 0.9124 (m) cc_final: 0.8875 (m) REVERT: A 840 TYR cc_start: 0.9208 (t80) cc_final: 0.8845 (t80) REVERT: A 842 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8214 (t80) REVERT: A 1045 LEU cc_start: 0.9341 (tp) cc_final: 0.8941 (tt) REVERT: A 1053 ASP cc_start: 0.8890 (t70) cc_final: 0.8489 (t0) REVERT: A 1056 PHE cc_start: 0.8953 (t80) cc_final: 0.8708 (t80) REVERT: A 1066 LYS cc_start: 0.9234 (mttt) cc_final: 0.9011 (mtpt) REVERT: A 1072 MET cc_start: 0.8054 (tmm) cc_final: 0.7663 (tmm) REVERT: B 491 LYS cc_start: 0.9266 (tttt) cc_final: 0.9002 (ptmm) REVERT: B 509 LEU cc_start: 0.9084 (mm) cc_final: 0.8784 (mm) REVERT: B 635 LYS cc_start: 0.9200 (tttt) cc_final: 0.8914 (ttmt) REVERT: B 720 MET cc_start: 0.8658 (mmp) cc_final: 0.8106 (mmm) REVERT: B 805 ASN cc_start: 0.8999 (m110) cc_final: 0.8511 (t0) REVERT: B 834 CYS cc_start: 0.9042 (m) cc_final: 0.8733 (m) REVERT: B 1053 ASP cc_start: 0.8779 (t70) cc_final: 0.8524 (t70) REVERT: B 1059 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8680 (mm-30) REVERT: B 1066 LYS cc_start: 0.9296 (mttt) cc_final: 0.9033 (mtpt) REVERT: B 1072 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6348 (ptp) REVERT: D 491 LYS cc_start: 0.9333 (tttt) cc_final: 0.9069 (ptmm) REVERT: D 704 LYS cc_start: 0.9562 (mttt) cc_final: 0.9305 (mttp) REVERT: D 709 MET cc_start: 0.8735 (ppp) cc_final: 0.8456 (tmm) REVERT: D 721 MET cc_start: 0.8318 (mmm) cc_final: 0.7779 (tmt) REVERT: D 776 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9075 (tt) REVERT: D 803 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7816 (tp) REVERT: D 808 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8785 (mm-30) REVERT: D 845 ASN cc_start: 0.8996 (t0) cc_final: 0.8191 (t0) REVERT: D 941 LEU cc_start: 0.9316 (tp) cc_final: 0.9067 (tp) REVERT: D 1053 ASP cc_start: 0.8782 (t70) cc_final: 0.8483 (t70) REVERT: D 1059 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8115 (mm-30) REVERT: D 1072 MET cc_start: 0.7975 (tmm) cc_final: 0.7532 (tmm) REVERT: C 491 LYS cc_start: 0.9360 (tttt) cc_final: 0.9091 (ptmm) REVERT: C 544 LEU cc_start: 0.9368 (mt) cc_final: 0.9130 (mt) REVERT: C 720 MET cc_start: 0.8524 (mmp) cc_final: 0.8232 (mmm) REVERT: C 721 MET cc_start: 0.8045 (tmm) cc_final: 0.7384 (tmm) REVERT: C 727 CYS cc_start: 0.9314 (t) cc_final: 0.9036 (t) REVERT: C 803 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 808 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8419 (mm-30) REVERT: C 816 ILE cc_start: 0.9472 (pt) cc_final: 0.9233 (pt) REVERT: C 834 CYS cc_start: 0.9287 (m) cc_final: 0.9042 (m) REVERT: C 842 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: C 848 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9060 (tp) REVERT: C 944 PHE cc_start: 0.9368 (t80) cc_final: 0.9009 (t80) REVERT: C 1053 ASP cc_start: 0.8950 (t70) cc_final: 0.8712 (t70) REVERT: C 1072 MET cc_start: 0.7903 (tmm) cc_final: 0.7459 (tmm) outliers start: 73 outliers final: 45 residues processed: 411 average time/residue: 0.1029 time to fit residues: 69.2136 Evaluate side-chains 401 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 347 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 chunk 210 optimal weight: 0.1980 chunk 145 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 907 GLN D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080034 restraints weight = 49104.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082541 restraints weight = 25166.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084257 restraints weight = 16326.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085187 restraints weight = 12237.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085879 restraints weight = 10259.501| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18096 Z= 0.113 Angle : 0.678 12.766 24520 Z= 0.317 Chirality : 0.041 0.144 2900 Planarity : 0.004 0.049 3008 Dihedral : 4.663 50.340 2385 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.25 % Allowed : 25.96 % Favored : 70.79 % 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: -0.04 (0.18), residues: 2208 helix: 0.52 (0.13), residues: 1584 sheet: 4.44 (0.74), residues: 40 loop : -1.73 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.012 0.001 TYR B 842 PHE 0.021 0.001 PHE B 944 TRP 0.022 0.001 TRP C 605 HIS 0.002 0.000 HIS D 933 Details of bonding type rmsd covalent geometry : bond 0.00253 (18096) covalent geometry : angle 0.67823 (24520) hydrogen bonds : bond 0.03222 ( 958) hydrogen bonds : angle 3.92068 ( 2838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 387 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9485 (mt) cc_final: 0.9218 (mt) REVERT: A 483 MET cc_start: 0.9143 (mmm) cc_final: 0.8761 (mmp) REVERT: A 491 LYS cc_start: 0.9430 (tttt) cc_final: 0.9143 (ptmm) REVERT: A 509 LEU cc_start: 0.8959 (mm) cc_final: 0.8686 (mm) REVERT: A 544 LEU cc_start: 0.9368 (mt) cc_final: 0.9106 (mt) REVERT: A 586 LEU cc_start: 0.9646 (tp) cc_final: 0.9329 (tp) REVERT: A 642 MET cc_start: 0.8778 (mtp) cc_final: 0.8544 (mtt) REVERT: A 704 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9316 (mttp) REVERT: A 709 MET cc_start: 0.8682 (ppp) cc_final: 0.8401 (tmm) REVERT: A 721 MET cc_start: 0.8465 (mmm) cc_final: 0.7852 (tmm) REVERT: A 808 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8520 (mm-30) REVERT: A 834 CYS cc_start: 0.9022 (m) cc_final: 0.8817 (m) REVERT: A 840 TYR cc_start: 0.9197 (t80) cc_final: 0.8820 (t80) REVERT: A 842 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8213 (t80) REVERT: A 851 GLN cc_start: 0.8691 (tt0) cc_final: 0.8368 (pt0) REVERT: A 978 MET cc_start: 0.8291 (ttm) cc_final: 0.7840 (ttp) REVERT: A 1045 LEU cc_start: 0.9356 (tp) cc_final: 0.8896 (tt) REVERT: A 1053 ASP cc_start: 0.8755 (t70) cc_final: 0.8345 (t0) REVERT: A 1056 PHE cc_start: 0.8924 (t80) cc_final: 0.8711 (t80) REVERT: A 1066 LYS cc_start: 0.9227 (mttt) cc_final: 0.9016 (mtpt) REVERT: A 1072 MET cc_start: 0.8004 (tmm) cc_final: 0.7665 (tmm) REVERT: B 491 LYS cc_start: 0.9149 (tttt) cc_final: 0.8915 (ptmm) REVERT: B 509 LEU cc_start: 0.8984 (mm) cc_final: 0.8713 (mm) REVERT: B 530 MET cc_start: 0.9570 (mmm) cc_final: 0.9362 (mmm) REVERT: B 635 LYS cc_start: 0.9216 (tttt) cc_final: 0.8896 (ttmt) REVERT: B 720 MET cc_start: 0.8558 (mmp) cc_final: 0.8041 (mmm) REVERT: B 805 ASN cc_start: 0.8917 (m110) cc_final: 0.8466 (t0) REVERT: B 834 CYS cc_start: 0.8913 (m) cc_final: 0.8644 (m) REVERT: B 1053 ASP cc_start: 0.8625 (t70) cc_final: 0.8369 (t70) REVERT: B 1066 LYS cc_start: 0.9257 (mttt) cc_final: 0.9001 (mtpt) REVERT: D 488 LEU cc_start: 0.9439 (mp) cc_final: 0.9208 (mp) REVERT: D 491 LYS cc_start: 0.9245 (tttt) cc_final: 0.9036 (ptmm) REVERT: D 586 LEU cc_start: 0.9629 (tp) cc_final: 0.9293 (tp) REVERT: D 704 LYS cc_start: 0.9559 (mttt) cc_final: 0.9317 (mttp) REVERT: D 709 MET cc_start: 0.8657 (ppp) cc_final: 0.8415 (tmm) REVERT: D 721 MET cc_start: 0.8196 (mmm) cc_final: 0.7751 (tmm) REVERT: D 776 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9105 (tt) REVERT: D 803 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7877 (tp) REVERT: D 808 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8757 (mm-30) REVERT: D 845 ASN cc_start: 0.8864 (t0) cc_final: 0.8003 (t0) REVERT: D 1053 ASP cc_start: 0.8644 (t70) cc_final: 0.8348 (t70) REVERT: D 1059 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 1060 LYS cc_start: 0.9406 (ptpp) cc_final: 0.8901 (ptpp) REVERT: D 1063 GLU cc_start: 0.8818 (tp30) cc_final: 0.8597 (tp30) REVERT: D 1073 GLU cc_start: 0.7688 (pm20) cc_final: 0.7434 (pm20) REVERT: C 491 LYS cc_start: 0.9287 (tttt) cc_final: 0.9068 (ptmm) REVERT: C 544 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt) REVERT: C 720 MET cc_start: 0.8369 (mmp) cc_final: 0.8137 (mmm) REVERT: C 721 MET cc_start: 0.7918 (tmm) cc_final: 0.7230 (tmm) REVERT: C 727 CYS cc_start: 0.9217 (t) cc_final: 0.8943 (t) REVERT: C 803 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 805 ASN cc_start: 0.8925 (m110) cc_final: 0.8625 (t0) REVERT: C 808 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8303 (mm-30) REVERT: C 816 ILE cc_start: 0.9494 (pt) cc_final: 0.9245 (pt) REVERT: C 834 CYS cc_start: 0.9183 (m) cc_final: 0.8973 (m) REVERT: C 842 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: C 848 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9036 (tp) REVERT: C 963 ASP cc_start: 0.8340 (m-30) cc_final: 0.8106 (m-30) REVERT: C 1053 ASP cc_start: 0.8819 (t70) cc_final: 0.8579 (t70) REVERT: C 1072 MET cc_start: 0.7845 (tmm) cc_final: 0.7422 (tmm) outliers start: 61 outliers final: 38 residues processed: 422 average time/residue: 0.1045 time to fit residues: 71.5875 Evaluate side-chains 397 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 131 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.0070 chunk 80 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN B 907 GLN B 933 HIS B 940 GLN D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C1047 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080137 restraints weight = 48690.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082598 restraints weight = 24917.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084269 restraints weight = 16042.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085197 restraints weight = 11980.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085861 restraints weight = 9964.855| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18096 Z= 0.119 Angle : 0.713 12.344 24520 Z= 0.329 Chirality : 0.042 0.206 2900 Planarity : 0.004 0.049 3008 Dihedral : 4.480 49.417 2381 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.20 % Allowed : 26.76 % Favored : 70.04 % 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: -0.00 (0.19), residues: 2208 helix: 0.53 (0.13), residues: 1584 sheet: 4.53 (0.73), residues: 40 loop : -1.68 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 919 TYR 0.019 0.001 TYR C 840 PHE 0.026 0.001 PHE C 944 TRP 0.020 0.001 TRP C 605 HIS 0.002 0.000 HIS D 933 Details of bonding type rmsd covalent geometry : bond 0.00277 (18096) covalent geometry : angle 0.71266 (24520) hydrogen bonds : bond 0.03224 ( 958) hydrogen bonds : angle 3.95356 ( 2838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 361 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9495 (mt) cc_final: 0.9229 (mt) REVERT: A 473 ARG cc_start: 0.8729 (pmt-80) cc_final: 0.8361 (pmt-80) REVERT: A 483 MET cc_start: 0.9177 (mmm) cc_final: 0.8780 (mmp) REVERT: A 491 LYS cc_start: 0.9428 (tttt) cc_final: 0.9151 (ptmm) REVERT: A 509 LEU cc_start: 0.8974 (mm) cc_final: 0.8697 (mm) REVERT: A 544 LEU cc_start: 0.9393 (mt) cc_final: 0.9126 (mt) REVERT: A 586 LEU cc_start: 0.9637 (tp) cc_final: 0.9321 (tp) REVERT: A 634 MET cc_start: 0.9498 (tpt) cc_final: 0.9290 (tpt) REVERT: A 642 MET cc_start: 0.8851 (mtp) cc_final: 0.8599 (mtt) REVERT: A 704 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9351 (mttp) REVERT: A 721 MET cc_start: 0.8537 (mmm) cc_final: 0.7872 (tmm) REVERT: A 808 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8524 (mm-30) REVERT: A 834 CYS cc_start: 0.9100 (m) cc_final: 0.8862 (m) REVERT: A 840 TYR cc_start: 0.9215 (t80) cc_final: 0.8859 (t80) REVERT: A 842 TYR cc_start: 0.8942 (m-80) cc_final: 0.8255 (t80) REVERT: A 851 GLN cc_start: 0.8682 (tt0) cc_final: 0.8437 (pt0) REVERT: A 1045 LEU cc_start: 0.9287 (tp) cc_final: 0.8827 (tt) REVERT: A 1053 ASP cc_start: 0.8811 (t70) cc_final: 0.8323 (t0) REVERT: A 1056 PHE cc_start: 0.8947 (t80) cc_final: 0.8736 (t80) REVERT: A 1065 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9124 (tp) REVERT: A 1072 MET cc_start: 0.8069 (tmm) cc_final: 0.7671 (tmm) REVERT: B 491 LYS cc_start: 0.9188 (tttt) cc_final: 0.8903 (ptmm) REVERT: B 509 LEU cc_start: 0.8983 (mm) cc_final: 0.8724 (mm) REVERT: B 530 MET cc_start: 0.9591 (mmm) cc_final: 0.9322 (mmm) REVERT: B 635 LYS cc_start: 0.9197 (tttt) cc_final: 0.8881 (ttmt) REVERT: B 720 MET cc_start: 0.8619 (mmp) cc_final: 0.8073 (mmm) REVERT: B 805 ASN cc_start: 0.8924 (m110) cc_final: 0.8466 (t0) REVERT: B 834 CYS cc_start: 0.9015 (m) cc_final: 0.8710 (m) REVERT: B 1053 ASP cc_start: 0.8690 (t70) cc_final: 0.8431 (t70) REVERT: D 491 LYS cc_start: 0.9269 (tttt) cc_final: 0.9063 (ptmm) REVERT: D 586 LEU cc_start: 0.9631 (tp) cc_final: 0.9307 (tp) REVERT: D 704 LYS cc_start: 0.9560 (mttt) cc_final: 0.9313 (mttp) REVERT: D 721 MET cc_start: 0.8275 (mmm) cc_final: 0.7760 (tmm) REVERT: D 776 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9078 (tt) REVERT: D 803 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (tp) REVERT: D 808 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8782 (mm-30) REVERT: D 842 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: D 844 MET cc_start: 0.9289 (mmt) cc_final: 0.9079 (mmm) REVERT: D 845 ASN cc_start: 0.8900 (t0) cc_final: 0.8055 (t0) REVERT: D 1053 ASP cc_start: 0.8708 (t70) cc_final: 0.8412 (t70) REVERT: D 1059 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 1060 LYS cc_start: 0.9428 (ptpp) cc_final: 0.8904 (ptpp) REVERT: D 1063 GLU cc_start: 0.8899 (tp30) cc_final: 0.8667 (tp30) REVERT: D 1072 MET cc_start: 0.7919 (tmm) cc_final: 0.7483 (tmm) REVERT: C 491 LYS cc_start: 0.9301 (tttt) cc_final: 0.9100 (ptmm) REVERT: C 523 MET cc_start: 0.8779 (mmt) cc_final: 0.8504 (tpp) REVERT: C 544 LEU cc_start: 0.9359 (mt) cc_final: 0.9120 (mt) REVERT: C 586 LEU cc_start: 0.9603 (tp) cc_final: 0.9387 (tp) REVERT: C 720 MET cc_start: 0.8443 (mmp) cc_final: 0.8220 (mmm) REVERT: C 721 MET cc_start: 0.8010 (tmm) cc_final: 0.7346 (tmm) REVERT: C 727 CYS cc_start: 0.9273 (t) cc_final: 0.8970 (t) REVERT: C 803 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8040 (tp) REVERT: C 805 ASN cc_start: 0.8967 (m110) cc_final: 0.8642 (t0) REVERT: C 808 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: C 816 ILE cc_start: 0.9472 (pt) cc_final: 0.9226 (pt) REVERT: C 834 CYS cc_start: 0.9259 (m) cc_final: 0.9022 (m) REVERT: C 842 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: C 848 LEU cc_start: 0.9305 (mp) cc_final: 0.9048 (tp) REVERT: C 963 ASP cc_start: 0.8403 (m-30) cc_final: 0.8153 (m-30) REVERT: C 1045 LEU cc_start: 0.9191 (tp) cc_final: 0.8943 (tt) REVERT: C 1053 ASP cc_start: 0.8905 (t70) cc_final: 0.8657 (t70) REVERT: C 1072 MET cc_start: 0.7899 (tmm) cc_final: 0.7474 (tmm) outliers start: 60 outliers final: 40 residues processed: 395 average time/residue: 0.1052 time to fit residues: 67.4593 Evaluate side-chains 395 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 195 optimal weight: 0.4980 chunk 223 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN B 933 HIS D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078809 restraints weight = 49199.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081258 restraints weight = 25641.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082921 restraints weight = 16747.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083941 restraints weight = 12626.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084685 restraints weight = 10496.917| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18096 Z= 0.129 Angle : 0.720 12.340 24520 Z= 0.337 Chirality : 0.043 0.160 2900 Planarity : 0.004 0.048 3008 Dihedral : 4.484 50.400 2381 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.36 % Allowed : 27.03 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 2208 helix: 0.54 (0.13), residues: 1580 sheet: 4.52 (0.72), residues: 40 loop : -1.69 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 919 TYR 0.022 0.001 TYR D 840 PHE 0.023 0.001 PHE C 944 TRP 0.032 0.001 TRP C 605 HIS 0.003 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00305 (18096) covalent geometry : angle 0.71998 (24520) hydrogen bonds : bond 0.03250 ( 958) hydrogen bonds : angle 3.99675 ( 2838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9488 (mt) cc_final: 0.9223 (mt) REVERT: A 473 ARG cc_start: 0.8712 (pmt-80) cc_final: 0.8339 (pmt-80) REVERT: A 483 MET cc_start: 0.9140 (mmm) cc_final: 0.8729 (mmp) REVERT: A 491 LYS cc_start: 0.9459 (tttt) cc_final: 0.9188 (ptmm) REVERT: A 509 LEU cc_start: 0.8970 (mm) cc_final: 0.8694 (mm) REVERT: A 544 LEU cc_start: 0.9396 (mt) cc_final: 0.9126 (mt) REVERT: A 586 LEU cc_start: 0.9627 (tp) cc_final: 0.9307 (tp) REVERT: A 642 MET cc_start: 0.8842 (mtp) cc_final: 0.8583 (mtt) REVERT: A 721 MET cc_start: 0.8553 (mmm) cc_final: 0.7879 (tmm) REVERT: A 808 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8523 (mm-30) REVERT: A 834 CYS cc_start: 0.9103 (m) cc_final: 0.8863 (m) REVERT: A 840 TYR cc_start: 0.9201 (t80) cc_final: 0.8848 (t80) REVERT: A 842 TYR cc_start: 0.8942 (m-80) cc_final: 0.8276 (t80) REVERT: A 851 GLN cc_start: 0.8732 (tt0) cc_final: 0.8460 (pt0) REVERT: A 978 MET cc_start: 0.8260 (ttm) cc_final: 0.7850 (ttp) REVERT: A 1045 LEU cc_start: 0.9296 (tp) cc_final: 0.8830 (tt) REVERT: A 1053 ASP cc_start: 0.8813 (t70) cc_final: 0.8334 (t0) REVERT: A 1056 PHE cc_start: 0.8949 (t80) cc_final: 0.8732 (t80) REVERT: A 1065 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9164 (tp) REVERT: B 491 LYS cc_start: 0.9200 (tttt) cc_final: 0.8915 (ptmm) REVERT: B 509 LEU cc_start: 0.9012 (mm) cc_final: 0.8752 (mm) REVERT: B 530 MET cc_start: 0.9605 (mmm) cc_final: 0.9397 (mmm) REVERT: B 635 LYS cc_start: 0.9202 (tttt) cc_final: 0.8878 (ttmt) REVERT: B 720 MET cc_start: 0.8628 (mmp) cc_final: 0.8105 (mmm) REVERT: B 805 ASN cc_start: 0.8922 (m110) cc_final: 0.8478 (t0) REVERT: B 834 CYS cc_start: 0.9017 (m) cc_final: 0.8722 (m) REVERT: B 1053 ASP cc_start: 0.8686 (t70) cc_final: 0.8431 (t70) REVERT: B 1066 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8989 (mtpt) REVERT: D 491 LYS cc_start: 0.9276 (tttt) cc_final: 0.9071 (ptmm) REVERT: D 586 LEU cc_start: 0.9634 (tp) cc_final: 0.9317 (tp) REVERT: D 704 LYS cc_start: 0.9552 (mttt) cc_final: 0.9315 (mttp) REVERT: D 721 MET cc_start: 0.8286 (mmm) cc_final: 0.7785 (tmm) REVERT: D 776 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9131 (tt) REVERT: D 803 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7825 (tp) REVERT: D 808 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8779 (mm-30) REVERT: D 842 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: D 844 MET cc_start: 0.9282 (mmt) cc_final: 0.9072 (mmm) REVERT: D 845 ASN cc_start: 0.8929 (t0) cc_final: 0.8073 (t0) REVERT: D 1049 TYR cc_start: 0.8697 (m-80) cc_final: 0.8481 (m-80) REVERT: D 1053 ASP cc_start: 0.8711 (t70) cc_final: 0.8424 (t70) REVERT: D 1059 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8437 (mm-30) REVERT: D 1063 GLU cc_start: 0.8847 (tp30) cc_final: 0.8615 (tp30) REVERT: D 1072 MET cc_start: 0.7934 (tmm) cc_final: 0.7412 (tmm) REVERT: C 544 LEU cc_start: 0.9361 (mt) cc_final: 0.9132 (mt) REVERT: C 586 LEU cc_start: 0.9607 (tp) cc_final: 0.9380 (tp) REVERT: C 720 MET cc_start: 0.8445 (mmp) cc_final: 0.8231 (mmm) REVERT: C 721 MET cc_start: 0.8013 (tmm) cc_final: 0.7353 (tmm) REVERT: C 727 CYS cc_start: 0.9257 (t) cc_final: 0.8963 (t) REVERT: C 803 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8050 (tp) REVERT: C 808 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: C 816 ILE cc_start: 0.9483 (pt) cc_final: 0.9239 (pt) REVERT: C 834 CYS cc_start: 0.9236 (m) cc_final: 0.9006 (m) REVERT: C 842 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: C 848 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9009 (tp) REVERT: C 1045 LEU cc_start: 0.9202 (tp) cc_final: 0.8935 (tt) REVERT: C 1053 ASP cc_start: 0.8891 (t70) cc_final: 0.8647 (t70) REVERT: C 1072 MET cc_start: 0.7908 (tmm) cc_final: 0.7483 (tmm) outliers start: 63 outliers final: 48 residues processed: 390 average time/residue: 0.1088 time to fit residues: 69.0108 Evaluate side-chains 392 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 336 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 913 LEU Chi-restraints excluded: chain D residue 923 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078359 restraints weight = 49305.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080820 restraints weight = 25911.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082467 restraints weight = 16988.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083633 restraints weight = 12802.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084169 restraints weight = 10586.400| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18096 Z= 0.135 Angle : 0.745 13.402 24520 Z= 0.347 Chirality : 0.043 0.190 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.493 51.151 2381 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.30 % Allowed : 27.99 % Favored : 68.71 % 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: -0.01 (0.19), residues: 2208 helix: 0.52 (0.13), residues: 1584 sheet: 4.47 (0.71), residues: 40 loop : -1.65 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 458 TYR 0.021 0.001 TYR C 840 PHE 0.023 0.001 PHE C 783 TRP 0.030 0.001 TRP C 605 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00320 (18096) covalent geometry : angle 0.74511 (24520) hydrogen bonds : bond 0.03287 ( 958) hydrogen bonds : angle 4.02610 ( 2838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9484 (mt) cc_final: 0.9217 (mt) REVERT: A 473 ARG cc_start: 0.8699 (pmt-80) cc_final: 0.8309 (pmt-80) REVERT: A 483 MET cc_start: 0.9135 (mmm) cc_final: 0.8738 (mmp) REVERT: A 491 LYS cc_start: 0.9456 (tttt) cc_final: 0.9188 (ptmm) REVERT: A 504 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8816 (tppp) REVERT: A 509 LEU cc_start: 0.8916 (mm) cc_final: 0.8648 (mm) REVERT: A 523 MET cc_start: 0.8925 (mmm) cc_final: 0.8095 (mmm) REVERT: A 544 LEU cc_start: 0.9355 (mt) cc_final: 0.9092 (mt) REVERT: A 577 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.6268 (p0) REVERT: A 586 LEU cc_start: 0.9607 (tp) cc_final: 0.9294 (tp) REVERT: A 642 MET cc_start: 0.8814 (mtp) cc_final: 0.8563 (mtt) REVERT: A 721 MET cc_start: 0.8531 (mmm) cc_final: 0.7879 (tmm) REVERT: A 808 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8517 (mm-30) REVERT: A 834 CYS cc_start: 0.9054 (m) cc_final: 0.8831 (m) REVERT: A 840 TYR cc_start: 0.9166 (t80) cc_final: 0.8831 (t80) REVERT: A 842 TYR cc_start: 0.8930 (m-80) cc_final: 0.8280 (t80) REVERT: A 851 GLN cc_start: 0.8778 (tt0) cc_final: 0.8548 (pt0) REVERT: A 1045 LEU cc_start: 0.9308 (tp) cc_final: 0.8852 (tt) REVERT: A 1053 ASP cc_start: 0.8767 (t70) cc_final: 0.8294 (t0) REVERT: A 1056 PHE cc_start: 0.8947 (t80) cc_final: 0.8728 (t80) REVERT: A 1065 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9232 (tp) REVERT: B 491 LYS cc_start: 0.9204 (tttt) cc_final: 0.8924 (ptmm) REVERT: B 509 LEU cc_start: 0.9020 (mm) cc_final: 0.8780 (mm) REVERT: B 530 MET cc_start: 0.9612 (mmm) cc_final: 0.9385 (mmm) REVERT: B 635 LYS cc_start: 0.9214 (tttt) cc_final: 0.8888 (ttmt) REVERT: B 720 MET cc_start: 0.8623 (mmp) cc_final: 0.8135 (mmm) REVERT: B 774 MET cc_start: 0.8818 (ttt) cc_final: 0.8590 (ptm) REVERT: B 805 ASN cc_start: 0.8874 (m110) cc_final: 0.8468 (t0) REVERT: B 834 CYS cc_start: 0.8993 (m) cc_final: 0.8705 (m) REVERT: B 1053 ASP cc_start: 0.8643 (t70) cc_final: 0.8394 (t70) REVERT: B 1066 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8990 (mtpt) REVERT: D 488 LEU cc_start: 0.9441 (mp) cc_final: 0.9226 (mp) REVERT: D 491 LYS cc_start: 0.9290 (tttt) cc_final: 0.9089 (ptmm) REVERT: D 586 LEU cc_start: 0.9635 (tp) cc_final: 0.9326 (tp) REVERT: D 704 LYS cc_start: 0.9553 (mttt) cc_final: 0.9343 (mttp) REVERT: D 721 MET cc_start: 0.8300 (mmm) cc_final: 0.7793 (tmm) REVERT: D 776 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9150 (tt) REVERT: D 803 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (tp) REVERT: D 808 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8762 (mm-30) REVERT: D 842 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: D 844 MET cc_start: 0.9271 (mmt) cc_final: 0.9038 (tpp) REVERT: D 845 ASN cc_start: 0.8902 (t0) cc_final: 0.8056 (t0) REVERT: D 1049 TYR cc_start: 0.8727 (m-80) cc_final: 0.8479 (m-80) REVERT: D 1053 ASP cc_start: 0.8676 (t70) cc_final: 0.8414 (t70) REVERT: D 1059 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8391 (mm-30) REVERT: D 1063 GLU cc_start: 0.8773 (tp30) cc_final: 0.8545 (tp30) REVERT: D 1072 MET cc_start: 0.8047 (tmm) cc_final: 0.7673 (tmm) REVERT: C 544 LEU cc_start: 0.9336 (mt) cc_final: 0.9114 (mt) REVERT: C 586 LEU cc_start: 0.9620 (tp) cc_final: 0.9397 (tp) REVERT: C 625 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8582 (mm-30) REVERT: C 720 MET cc_start: 0.8441 (mmp) cc_final: 0.8215 (mmm) REVERT: C 721 MET cc_start: 0.7984 (tmm) cc_final: 0.7280 (tmm) REVERT: C 727 CYS cc_start: 0.9225 (t) cc_final: 0.8939 (t) REVERT: C 803 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 808 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: C 816 ILE cc_start: 0.9481 (pt) cc_final: 0.9237 (pt) REVERT: C 834 CYS cc_start: 0.9183 (m) cc_final: 0.8966 (m) REVERT: C 840 TYR cc_start: 0.9223 (t80) cc_final: 0.8923 (t80) REVERT: C 842 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: C 848 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8985 (tp) REVERT: C 1045 LEU cc_start: 0.9191 (tp) cc_final: 0.8917 (tt) REVERT: C 1053 ASP cc_start: 0.8851 (t70) cc_final: 0.8605 (t70) REVERT: C 1072 MET cc_start: 0.7844 (tmm) cc_final: 0.7503 (tmm) outliers start: 62 outliers final: 46 residues processed: 392 average time/residue: 0.1086 time to fit residues: 68.2822 Evaluate side-chains 394 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 923 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 848 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN B1070 GLN D 481 HIS ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** 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 = 0.3596 r_free = 0.3596 target = 0.099912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078157 restraints weight = 49484.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080621 restraints weight = 26014.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082287 restraints weight = 17067.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083331 restraints weight = 12879.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084145 restraints weight = 10688.823| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18096 Z= 0.137 Angle : 0.748 13.024 24520 Z= 0.350 Chirality : 0.043 0.156 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.380 41.542 2379 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.99 % Allowed : 28.73 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.02 (0.18), residues: 2208 helix: 0.52 (0.13), residues: 1580 sheet: 4.46 (0.71), residues: 40 loop : -1.64 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 464 TYR 0.023 0.001 TYR D 840 PHE 0.022 0.001 PHE C 944 TRP 0.029 0.001 TRP C 605 HIS 0.003 0.001 HIS D 933 Details of bonding type rmsd covalent geometry : bond 0.00327 (18096) covalent geometry : angle 0.74814 (24520) hydrogen bonds : bond 0.03263 ( 958) hydrogen bonds : angle 4.02919 ( 2838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.27 seconds wall clock time: 49 minutes 10.80 seconds (2950.80 seconds total)