Starting phenix.real_space_refine on Thu Mar 5 10:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wta_32773/03_2026/7wta_32773.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 148 5.16 5 C 13396 2.51 5 N 3616 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 21080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.82, per 1000 atoms: 0.23 Number of scatterers: 21080 At special positions: 0 Unit cell: (161.7, 147.4, 127.6, 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 148 16.00 O 3920 8.00 N 3616 7.00 C 13396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.03 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 16 sheets defined 47.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 560 removed outlier: 4.208A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.511A pdb=" N ALA A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.172A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.728A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.605A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.711A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.535A pdb=" N ALA A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 828 through 843 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.829A pdb=" N ALA A 852 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 886 through 901 removed outlier: 4.002A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 894 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 925 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.735A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.667A pdb=" N PHE A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.195A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.873A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.661A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.614A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.849A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.678A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 790 " --> pdb=" O CYS B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.701A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 3.966A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 870 through 881 Processing helix chain 'B' and resid 886 through 893 removed outlier: 3.699A pdb=" N VAL B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 891 " --> pdb=" O PHE B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.820A pdb=" N GLN B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 950 removed outlier: 3.667A pdb=" N GLY B 950 " --> pdb=" O GLU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.542A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 987 through 999 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 3.512A pdb=" N PHE B1017 " --> pdb=" O TYR B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.798A pdb=" N LEU C 500 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.048A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 622 through 632 removed outlier: 4.331A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 669 Processing helix chain 'C' and resid 682 through 697 Processing helix chain 'C' and resid 719 through 734 Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.541A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 removed outlier: 4.176A pdb=" N GLY C 790 " --> pdb=" O CYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.787A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 843 removed outlier: 3.828A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 860 through 865 Processing helix chain 'C' and resid 867 through 869 No H-bonds generated for 'chain 'C' and resid 867 through 869' Processing helix chain 'C' and resid 870 through 882 Processing helix chain 'C' and resid 886 through 902 removed outlier: 4.177A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 925 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 960 through 969 removed outlier: 3.981A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 999 removed outlier: 3.663A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 496 through 511 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.582A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 584 through 598 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 610 through 617 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.515A pdb=" N ARG D 626 " --> pdb=" O CYS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 733 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.655A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 removed outlier: 4.047A pdb=" N LEU D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 845 removed outlier: 3.723A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 853 removed outlier: 3.911A pdb=" N ASP D 849 " --> pdb=" O ALA D 846 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N CYS D 850 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR D 851 " --> pdb=" O PHE D 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 852 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 882 Processing helix chain 'D' and resid 883 through 885 No H-bonds generated for 'chain 'D' and resid 883 through 885' Processing helix chain 'D' and resid 886 through 901 removed outlier: 3.506A pdb=" N LYS D 892 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 901 " --> pdb=" O ALA D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 removed outlier: 3.705A pdb=" N VAL D 945 " --> pdb=" O PRO D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.846A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 3.627A pdb=" N PHE D1017 " --> pdb=" O TYR D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 7.288A pdb=" N LEU A 565 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N GLU A 605 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP A 567 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A 639 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ARG A 675 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET A 641 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE A 677 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 643 " --> pdb=" O PHE A 677 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 674 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 768 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASP A 795 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 770 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 6.726A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 4.010A pdb=" N LEU A1175 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A1174 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A1160 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A1155 " --> pdb=" O VAL A1131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1149 removed outlier: 3.587A pdb=" N THR A1147 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1122 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A1141 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A1120 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 567 removed outlier: 7.009A pdb=" N LEU B 565 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 674 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.851A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1113 removed outlier: 6.824A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B1174 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B1160 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU B1176 " --> pdb=" O ARG B1158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B1158 " --> pdb=" O GLU B1176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1119 through 1123 removed outlier: 3.574A pdb=" N LYS B1119 " --> pdb=" O SER B1141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B1138 " --> pdb=" O VAL B1149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 699 through 702 removed outlier: 6.689A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 565 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 795 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR C 772 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1046 through 1051 removed outlier: 3.934A pdb=" N GLU C1046 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1062 " --> pdb=" O GLU C1046 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1111 through 1112 removed outlier: 3.949A pdb=" N LEU C1175 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C1158 " --> pdb=" O GLU C1176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1146 through 1151 removed outlier: 6.751A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C1135 " --> pdb=" O SER C1151 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C1141 " --> pdb=" O LYS C1119 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C1119 " --> pdb=" O SER C1141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 564 through 567 removed outlier: 7.045A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU D 768 " --> pdb=" O VAL D 793 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASP D 795 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE D 770 " --> pdb=" O ASP D 795 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.836A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.510A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 7.968A pdb=" N ILE D1112 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D1174 " --> pdb=" O ILE D1112 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE D1174 " --> pdb=" O VAL D1160 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D1160 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU D1176 " --> pdb=" O ARG D1158 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D1156 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.204A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS D1138 " --> pdb=" O VAL D1149 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2601 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: 3.83 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3570 1.31 - 1.43: 5335 1.43 - 1.56: 12365 1.56 - 1.69: 26 1.69 - 1.82: 260 Bond restraints: 21556 Sorted by residual: bond pdb=" C6 BTI A1900 " pdb=" S1 BTI A1900 " ideal model delta sigma weight residual 1.811 1.440 0.371 2.00e-02 2.50e+03 3.44e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.442 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI B1900 " pdb=" S1 BTI B1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C3 BTI B1900 " pdb=" N3 BTI B1900 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 21551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.80: 29199 6.80 - 13.60: 13 13.60 - 20.40: 4 20.40 - 27.20: 2 27.20 - 34.00: 2 Bond angle restraints: 29220 Sorted by residual: angle pdb=" C10 BTI C1900 " pdb=" C11 BTI C1900 " pdb=" O11 BTI C1900 " ideal model delta sigma weight residual 125.49 91.49 34.00 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C10 BTI B1900 " pdb=" C11 BTI B1900 " pdb=" O11 BTI B1900 " ideal model delta sigma weight residual 125.49 92.99 32.50 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 BTI A1900 " pdb=" C11 BTI A1900 " pdb=" O11 BTI A1900 " ideal model delta sigma weight residual 125.49 99.42 26.07 3.00e+00 1.11e-01 7.55e+01 angle pdb=" C10 BTI D1900 " pdb=" C11 BTI D1900 " pdb=" O11 BTI D1900 " ideal model delta sigma weight residual 125.49 101.36 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" C2 BTI B1900 " pdb=" S1 BTI B1900 " pdb=" C6 BTI B1900 " ideal model delta sigma weight residual 89.29 106.58 -17.29 3.00e+00 1.11e-01 3.32e+01 ... (remaining 29215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11916 17.47 - 34.93: 1006 34.93 - 52.40: 179 52.40 - 69.86: 20 69.86 - 87.33: 15 Dihedral angle restraints: 13136 sinusoidal: 5300 harmonic: 7836 Sorted by residual: dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 176.35 -83.35 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 142.68 -49.68 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA CYS B 786 " pdb=" C CYS B 786 " pdb=" N ALA B 787 " pdb=" CA ALA B 787 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 13133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2410 0.041 - 0.083: 614 0.083 - 0.124: 220 0.124 - 0.166: 15 0.166 - 0.207: 5 Chirality restraints: 3264 Sorted by residual: chirality pdb=" C5 BTI C1900 " pdb=" C4 BTI C1900 " pdb=" C6 BTI C1900 " pdb=" N3 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.73 2.94 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5 BTI A1900 " pdb=" C4 BTI A1900 " pdb=" C6 BTI A1900 " pdb=" N3 BTI A1900 " both_signs ideal model delta sigma weight residual False 2.73 2.92 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" C4 BTI C1900 " pdb=" C2 BTI C1900 " pdb=" C5 BTI C1900 " pdb=" N2 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.75 2.57 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3261 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 535 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO D 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 536 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 807 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 808 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 807 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.64e+00 pdb=" N PRO D 808 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 808 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 808 " -0.022 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1086 2.72 - 3.26: 23479 3.26 - 3.81: 37347 3.81 - 4.35: 43228 4.35 - 4.90: 70120 Nonbonded interactions: 175260 Sorted by model distance: nonbonded pdb=" O TYR B 593 " pdb=" ND2 ASN B 597 " model vdw 2.171 3.120 nonbonded pdb=" OD2 ASP A 613 " pdb=" OH TYR A 651 " model vdw 2.183 3.040 nonbonded pdb=" NE2 GLN A1075 " pdb=" OG SER A1086 " model vdw 2.185 3.120 nonbonded pdb=" OG SER D1066 " pdb=" O GLN D1075 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU B 961 " pdb=" NH2 ARG B 964 " model vdw 2.188 3.120 ... (remaining 175255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.720 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.635 21565 Z= 0.594 Angle : 0.822 33.998 29228 Z= 0.394 Chirality : 0.042 0.207 3264 Planarity : 0.005 0.083 3828 Dihedral : 13.247 87.331 8092 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.21 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1116 sheet: -0.33 (0.28), residues: 344 loop : -1.39 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1070 TYR 0.018 0.002 TYR B 951 PHE 0.024 0.002 PHE C1078 TRP 0.016 0.002 TRP A 838 HIS 0.005 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00816 (21556) covalent geometry : angle 0.82048 (29220) SS BOND : bond 0.00711 ( 4) SS BOND : angle 3.08513 ( 8) hydrogen bonds : bond 0.18873 ( 882) hydrogen bonds : angle 7.62153 ( 2601) Misc. bond : bond 0.28416 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9522 (mmp) cc_final: 0.9147 (mmm) REVERT: A 566 MET cc_start: 0.5803 (ppp) cc_final: 0.5589 (ppp) REVERT: A 1166 MET cc_start: 0.8807 (ptp) cc_final: 0.8289 (pmm) REVERT: B 641 MET cc_start: 0.8239 (tmm) cc_final: 0.7886 (ppp) REVERT: B 686 MET cc_start: 0.9269 (mpp) cc_final: 0.9000 (mpp) REVERT: B 724 MET cc_start: 0.8967 (mmt) cc_final: 0.8398 (mmm) REVERT: B 1116 MET cc_start: 0.8360 (mmm) cc_final: 0.7914 (ppp) REVERT: B 1145 MET cc_start: 0.6365 (ptt) cc_final: 0.5686 (ptt) REVERT: C 754 MET cc_start: 0.9467 (ppp) cc_final: 0.9134 (ppp) REVERT: C 755 LEU cc_start: 0.9704 (mt) cc_final: 0.9327 (mt) REVERT: C 783 MET cc_start: 0.9073 (tpp) cc_final: 0.8863 (tpp) REVERT: C 804 MET cc_start: 0.8608 (tpp) cc_final: 0.8143 (tpp) REVERT: C 921 MET cc_start: 0.9576 (tpp) cc_final: 0.9376 (tpp) REVERT: C 1145 MET cc_start: 0.5515 (pmm) cc_final: 0.4796 (pmm) REVERT: D 574 HIS cc_start: 0.8922 (m-70) cc_final: 0.8687 (m170) REVERT: D 604 MET cc_start: 0.8388 (tpt) cc_final: 0.8120 (tpp) REVERT: D 810 MET cc_start: 0.9017 (mmp) cc_final: 0.8440 (mmm) REVERT: D 881 MET cc_start: 0.9230 (mmp) cc_final: 0.9028 (mmm) REVERT: D 947 PHE cc_start: 0.9254 (t80) cc_final: 0.9046 (t80) REVERT: D 1098 MET cc_start: 0.6401 (mmt) cc_final: 0.6198 (mmt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1432 time to fit residues: 38.2092 Evaluate side-chains 144 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 ASN C 899 GLN ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 HIS ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.035287 restraints weight = 231044.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.035946 restraints weight = 181606.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.036444 restraints weight = 151558.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.036820 restraints weight = 132007.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.037096 restraints weight = 118679.153| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21565 Z= 0.130 Angle : 0.648 9.323 29228 Z= 0.322 Chirality : 0.043 0.268 3264 Planarity : 0.005 0.057 3828 Dihedral : 5.354 58.677 3016 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 0.35 % Allowed : 6.87 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2728 helix: 0.68 (0.16), residues: 1164 sheet: -0.09 (0.29), residues: 338 loop : -1.42 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 842 TYR 0.014 0.002 TYR B 834 PHE 0.014 0.001 PHE B 947 TRP 0.019 0.001 TRP A 838 HIS 0.006 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00282 (21556) covalent geometry : angle 0.64730 (29220) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.78840 ( 8) hydrogen bonds : bond 0.04330 ( 882) hydrogen bonds : angle 6.02316 ( 2601) Misc. bond : bond 0.00415 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9558 (mmp) cc_final: 0.9133 (mmm) REVERT: A 566 MET cc_start: 0.5604 (ppp) cc_final: 0.5348 (ppp) REVERT: A 854 MET cc_start: 0.6186 (tmm) cc_final: 0.5697 (tmm) REVERT: A 900 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7979 (mmt) REVERT: A 1012 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6437 (ptp) REVERT: A 1153 MET cc_start: 0.8348 (ppp) cc_final: 0.7931 (ppp) REVERT: A 1166 MET cc_start: 0.8590 (ptp) cc_final: 0.7998 (pmm) REVERT: B 508 MET cc_start: 0.9051 (mmp) cc_final: 0.8837 (mmp) REVERT: B 566 MET cc_start: 0.8153 (tpp) cc_final: 0.7946 (tpp) REVERT: B 671 MET cc_start: 0.6656 (tpt) cc_final: 0.6318 (tpt) REVERT: B 686 MET cc_start: 0.9168 (mpp) cc_final: 0.8873 (mpp) REVERT: B 1145 MET cc_start: 0.6513 (ptt) cc_final: 0.5609 (ptt) REVERT: C 508 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8231 (mmp) REVERT: C 754 MET cc_start: 0.9296 (ppp) cc_final: 0.8906 (ppp) REVERT: C 755 LEU cc_start: 0.9651 (mt) cc_final: 0.9132 (mt) REVERT: C 783 MET cc_start: 0.9018 (tpp) cc_final: 0.8776 (tpp) REVERT: C 804 MET cc_start: 0.8539 (tpp) cc_final: 0.8076 (tpp) REVERT: C 881 MET cc_start: 0.9274 (tpp) cc_final: 0.9051 (tpp) REVERT: D 508 MET cc_start: 0.9197 (mmp) cc_final: 0.8978 (mmp) REVERT: D 574 HIS cc_start: 0.8879 (m-70) cc_final: 0.8660 (m90) REVERT: D 604 MET cc_start: 0.8114 (tpt) cc_final: 0.7752 (tpp) REVERT: D 730 LEU cc_start: 0.8099 (tp) cc_final: 0.7893 (mm) REVERT: D 810 MET cc_start: 0.9011 (mmp) cc_final: 0.8566 (mmm) REVERT: D 854 MET cc_start: 0.8083 (ttt) cc_final: 0.7727 (ttt) REVERT: D 881 MET cc_start: 0.9338 (mmp) cc_final: 0.8964 (mmm) REVERT: D 947 PHE cc_start: 0.9159 (t80) cc_final: 0.8955 (t80) REVERT: D 1098 MET cc_start: 0.6540 (mmt) cc_final: 0.6307 (mmt) outliers start: 8 outliers final: 3 residues processed: 161 average time/residue: 0.1369 time to fit residues: 36.1075 Evaluate side-chains 151 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 241 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 190 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A1135 GLN B 510 ASN B 669 ASN C 510 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 873 ASN ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.045770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.034268 restraints weight = 244069.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.034857 restraints weight = 193687.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.035278 restraints weight = 162994.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.035605 restraints weight = 143322.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.035877 restraints weight = 130165.368| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21565 Z= 0.199 Angle : 0.659 10.144 29228 Z= 0.332 Chirality : 0.041 0.148 3264 Planarity : 0.005 0.049 3828 Dihedral : 5.255 53.654 3016 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 0.89 % Allowed : 10.11 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2728 helix: 0.66 (0.16), residues: 1166 sheet: -0.16 (0.29), residues: 338 loop : -1.43 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1054 TYR 0.017 0.002 TYR A 834 PHE 0.017 0.002 PHE A1077 TRP 0.022 0.002 TRP A 838 HIS 0.006 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00411 (21556) covalent geometry : angle 0.65900 (29220) SS BOND : bond 0.01424 ( 4) SS BOND : angle 1.25370 ( 8) hydrogen bonds : bond 0.04073 ( 882) hydrogen bonds : angle 5.97463 ( 2601) Misc. bond : bond 0.00264 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9520 (mmp) cc_final: 0.9077 (mmm) REVERT: A 1106 LYS cc_start: 0.9565 (tptp) cc_final: 0.9241 (mmmt) REVERT: A 1153 MET cc_start: 0.8169 (ppp) cc_final: 0.7695 (ppp) REVERT: A 1166 MET cc_start: 0.8553 (ptp) cc_final: 0.7997 (pmm) REVERT: B 508 MET cc_start: 0.9164 (mmp) cc_final: 0.8873 (mmp) REVERT: B 566 MET cc_start: 0.8657 (tpp) cc_final: 0.8431 (tpp) REVERT: B 616 MET cc_start: 0.8035 (mmp) cc_final: 0.7714 (mmp) REVERT: B 671 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6685 (tpt) REVERT: B 686 MET cc_start: 0.9267 (mpp) cc_final: 0.9026 (mpp) REVERT: B 1145 MET cc_start: 0.6735 (ptt) cc_final: 0.5754 (ptt) REVERT: C 754 MET cc_start: 0.9394 (ppp) cc_final: 0.8940 (ppp) REVERT: C 755 LEU cc_start: 0.9689 (mt) cc_final: 0.9240 (mt) REVERT: C 783 MET cc_start: 0.9158 (tpp) cc_final: 0.8888 (tpp) REVERT: C 804 MET cc_start: 0.8639 (tpp) cc_final: 0.8343 (tpp) REVERT: D 574 HIS cc_start: 0.9162 (m-70) cc_final: 0.8912 (m-70) REVERT: D 604 MET cc_start: 0.8249 (tpt) cc_final: 0.7904 (tpp) REVERT: D 616 MET cc_start: 0.8206 (mmp) cc_final: 0.7918 (mmp) REVERT: D 810 MET cc_start: 0.9117 (mmp) cc_final: 0.8687 (mmm) REVERT: D 881 MET cc_start: 0.9380 (mmp) cc_final: 0.9055 (mmm) REVERT: D 1098 MET cc_start: 0.6570 (mmt) cc_final: 0.6352 (mmt) REVERT: D 1153 MET cc_start: 0.8847 (pmm) cc_final: 0.8426 (pmm) outliers start: 20 outliers final: 11 residues processed: 170 average time/residue: 0.1355 time to fit residues: 37.2302 Evaluate side-chains 161 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 752 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 263 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A 934 GLN A 998 HIS ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS D 899 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.044706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.033041 restraints weight = 243945.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.033690 restraints weight = 188910.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.034154 restraints weight = 156486.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.034426 restraints weight = 135804.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.034702 restraints weight = 120861.177| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21565 Z= 0.213 Angle : 0.682 10.731 29228 Z= 0.344 Chirality : 0.042 0.150 3264 Planarity : 0.005 0.048 3828 Dihedral : 5.447 55.533 3016 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 1.55 % Allowed : 12.50 % Favored : 85.95 % 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: -0.66 (0.16), residues: 2728 helix: 0.50 (0.15), residues: 1178 sheet: -0.28 (0.29), residues: 352 loop : -1.41 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1054 TYR 0.016 0.002 TYR B 951 PHE 0.019 0.002 PHE B 763 TRP 0.017 0.002 TRP A 624 HIS 0.007 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00438 (21556) covalent geometry : angle 0.68181 (29220) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.14182 ( 8) hydrogen bonds : bond 0.03866 ( 882) hydrogen bonds : angle 5.93254 ( 2601) Misc. bond : bond 0.00031 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9526 (mmp) cc_final: 0.9043 (mmp) REVERT: A 566 MET cc_start: 0.5301 (ppp) cc_final: 0.4954 (ppp) REVERT: A 804 MET cc_start: 0.8633 (tpp) cc_final: 0.8047 (tpp) REVERT: A 854 MET cc_start: 0.6418 (tmm) cc_final: 0.5862 (tmm) REVERT: A 921 MET cc_start: 0.7875 (ptt) cc_final: 0.7401 (ppp) REVERT: A 1106 LYS cc_start: 0.9571 (tptp) cc_final: 0.9274 (mmmt) REVERT: A 1153 MET cc_start: 0.8308 (ppp) cc_final: 0.7591 (ppp) REVERT: A 1166 MET cc_start: 0.8532 (ptp) cc_final: 0.8050 (pmm) REVERT: B 508 MET cc_start: 0.9095 (mmp) cc_final: 0.8843 (mmp) REVERT: B 566 MET cc_start: 0.8360 (tpp) cc_final: 0.7855 (tpp) REVERT: B 671 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6750 (tpt) REVERT: B 934 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: B 959 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5381 (p90) REVERT: B 1012 MET cc_start: 0.8367 (pmm) cc_final: 0.7988 (pmm) REVERT: B 1078 PHE cc_start: 0.8881 (m-80) cc_final: 0.8680 (m-80) REVERT: B 1116 MET cc_start: 0.8098 (mmt) cc_final: 0.7136 (ptm) REVERT: B 1145 MET cc_start: 0.6582 (ptt) cc_final: 0.6268 (ptt) REVERT: C 754 MET cc_start: 0.9389 (ppp) cc_final: 0.9120 (ppp) REVERT: C 783 MET cc_start: 0.9046 (tpp) cc_final: 0.8757 (tpp) REVERT: C 804 MET cc_start: 0.8767 (tpp) cc_final: 0.8433 (tpp) REVERT: C 881 MET cc_start: 0.9132 (tpp) cc_final: 0.8775 (tpp) REVERT: D 566 MET cc_start: 0.5806 (ttt) cc_final: 0.5535 (tpp) REVERT: D 604 MET cc_start: 0.8278 (tpt) cc_final: 0.7882 (tpp) REVERT: D 616 MET cc_start: 0.8166 (mmp) cc_final: 0.7936 (mmp) REVERT: D 810 MET cc_start: 0.9118 (mmp) cc_final: 0.8665 (mmm) REVERT: D 854 MET cc_start: 0.8256 (ttt) cc_final: 0.7944 (ttt) REVERT: D 881 MET cc_start: 0.9458 (mmp) cc_final: 0.9240 (mmm) outliers start: 35 outliers final: 17 residues processed: 174 average time/residue: 0.1317 time to fit residues: 37.8385 Evaluate side-chains 163 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 145 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.045126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.033331 restraints weight = 238497.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.033974 restraints weight = 185856.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.034457 restraints weight = 154845.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.034827 restraints weight = 134953.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.035081 restraints weight = 120886.499| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21565 Z= 0.144 Angle : 0.646 11.181 29228 Z= 0.317 Chirality : 0.042 0.174 3264 Planarity : 0.004 0.043 3828 Dihedral : 5.334 59.438 3016 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 1.64 % Allowed : 13.70 % Favored : 84.66 % 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: -0.53 (0.16), residues: 2728 helix: 0.69 (0.16), residues: 1170 sheet: -0.29 (0.28), residues: 356 loop : -1.41 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 977 TYR 0.012 0.002 TYR B 837 PHE 0.013 0.001 PHE A 553 TRP 0.014 0.001 TRP A 838 HIS 0.005 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00309 (21556) covalent geometry : angle 0.64579 (29220) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.12868 ( 8) hydrogen bonds : bond 0.03501 ( 882) hydrogen bonds : angle 5.70211 ( 2601) Misc. bond : bond 0.00046 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9555 (mmp) cc_final: 0.9038 (mmp) REVERT: A 641 MET cc_start: 0.8073 (tmm) cc_final: 0.7866 (tmm) REVERT: A 690 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7660 (mmm) REVERT: A 921 MET cc_start: 0.7864 (ptt) cc_final: 0.7447 (ppp) REVERT: A 1106 LYS cc_start: 0.9588 (tptp) cc_final: 0.9305 (mmmt) REVERT: A 1153 MET cc_start: 0.8304 (ppp) cc_final: 0.7650 (ppp) REVERT: A 1166 MET cc_start: 0.8536 (ptp) cc_final: 0.8056 (pmm) REVERT: B 508 MET cc_start: 0.9033 (mmp) cc_final: 0.8798 (mmp) REVERT: B 566 MET cc_start: 0.8192 (tpp) cc_final: 0.7793 (tpp) REVERT: B 616 MET cc_start: 0.7920 (mmp) cc_final: 0.7650 (mmp) REVERT: B 671 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6678 (tpt) REVERT: B 959 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5717 (p90) REVERT: B 1116 MET cc_start: 0.7928 (mmt) cc_final: 0.7102 (ptm) REVERT: B 1145 MET cc_start: 0.6611 (ptt) cc_final: 0.6356 (ptt) REVERT: C 754 MET cc_start: 0.9401 (ppp) cc_final: 0.9139 (ppp) REVERT: C 783 MET cc_start: 0.9030 (tpp) cc_final: 0.8725 (tpp) REVERT: C 804 MET cc_start: 0.8712 (tpp) cc_final: 0.8401 (tpp) REVERT: D 604 MET cc_start: 0.8256 (tpt) cc_final: 0.7836 (tpp) REVERT: D 616 MET cc_start: 0.8145 (mmp) cc_final: 0.7903 (mmp) REVERT: D 729 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5393 (pm20) REVERT: D 746 LEU cc_start: 0.9369 (mt) cc_final: 0.9133 (pt) REVERT: D 810 MET cc_start: 0.9104 (mmp) cc_final: 0.8629 (mmm) REVERT: D 854 MET cc_start: 0.8400 (ttt) cc_final: 0.8183 (ttt) REVERT: D 881 MET cc_start: 0.9441 (mmp) cc_final: 0.9234 (mmm) outliers start: 37 outliers final: 20 residues processed: 177 average time/residue: 0.1313 time to fit residues: 38.8732 Evaluate side-chains 165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 188 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 270 optimal weight: 0.2980 chunk 200 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 256 optimal weight: 0.3980 chunk 138 optimal weight: 0.1980 chunk 197 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN C 559 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.034118 restraints weight = 232001.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.034746 restraints weight = 179040.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.035304 restraints weight = 146932.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.035664 restraints weight = 127524.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.035950 restraints weight = 114252.099| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21565 Z= 0.108 Angle : 0.641 10.936 29228 Z= 0.309 Chirality : 0.042 0.174 3264 Planarity : 0.004 0.041 3828 Dihedral : 5.144 56.821 3016 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 1.37 % Allowed : 14.85 % Favored : 83.78 % 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: -0.41 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1170 sheet: -0.01 (0.29), residues: 328 loop : -1.43 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1054 TYR 0.013 0.001 TYR B 834 PHE 0.011 0.001 PHE C1078 TRP 0.011 0.001 TRP A 838 HIS 0.005 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00238 (21556) covalent geometry : angle 0.64063 (29220) SS BOND : bond 0.00291 ( 4) SS BOND : angle 1.09683 ( 8) hydrogen bonds : bond 0.03284 ( 882) hydrogen bonds : angle 5.41133 ( 2601) Misc. bond : bond 0.00032 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9534 (mmp) cc_final: 0.9055 (mmp) REVERT: A 690 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7620 (mmm) REVERT: A 804 MET cc_start: 0.8594 (tpp) cc_final: 0.8152 (mmm) REVERT: A 854 MET cc_start: 0.6194 (tmm) cc_final: 0.5507 (tmm) REVERT: A 921 MET cc_start: 0.7784 (ptt) cc_final: 0.7574 (ppp) REVERT: A 1106 LYS cc_start: 0.9581 (tptp) cc_final: 0.9284 (mmmt) REVERT: A 1153 MET cc_start: 0.8250 (ppp) cc_final: 0.7713 (ppp) REVERT: A 1166 MET cc_start: 0.8571 (ptp) cc_final: 0.8049 (pmm) REVERT: B 508 MET cc_start: 0.9022 (mmp) cc_final: 0.8748 (mmp) REVERT: B 566 MET cc_start: 0.8211 (tpp) cc_final: 0.7842 (tpp) REVERT: B 616 MET cc_start: 0.7649 (mmp) cc_final: 0.7411 (mmp) REVERT: B 671 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6620 (tpt) REVERT: B 934 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: B 959 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5633 (p90) REVERT: B 1012 MET cc_start: 0.8353 (pmm) cc_final: 0.7950 (pmm) REVERT: B 1116 MET cc_start: 0.7855 (mmt) cc_final: 0.7078 (ptm) REVERT: B 1145 MET cc_start: 0.6597 (ptt) cc_final: 0.6293 (ptt) REVERT: C 508 MET cc_start: 0.8735 (mmt) cc_final: 0.7845 (mmt) REVERT: C 754 MET cc_start: 0.9405 (ppp) cc_final: 0.9153 (ppp) REVERT: D 604 MET cc_start: 0.8177 (tpt) cc_final: 0.7797 (tpp) REVERT: D 616 MET cc_start: 0.8053 (mmp) cc_final: 0.7812 (mmp) REVERT: D 706 TYR cc_start: 0.6599 (t80) cc_final: 0.5742 (t80) REVERT: D 730 LEU cc_start: 0.8221 (tp) cc_final: 0.7954 (mm) REVERT: D 746 LEU cc_start: 0.9282 (mt) cc_final: 0.8900 (pt) REVERT: D 810 MET cc_start: 0.9010 (mmp) cc_final: 0.8518 (mmm) REVERT: D 854 MET cc_start: 0.8413 (ttt) cc_final: 0.8163 (ttt) REVERT: D 881 MET cc_start: 0.9429 (mmp) cc_final: 0.9213 (mmm) outliers start: 31 outliers final: 17 residues processed: 169 average time/residue: 0.1325 time to fit residues: 36.8325 Evaluate side-chains 162 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 113 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 197 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 HIS ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.032507 restraints weight = 241491.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.033026 restraints weight = 193620.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.033469 restraints weight = 156930.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.033844 restraints weight = 134751.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.034053 restraints weight = 120459.406| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 21565 Z= 0.228 Angle : 0.731 10.558 29228 Z= 0.363 Chirality : 0.043 0.328 3264 Planarity : 0.005 0.046 3828 Dihedral : 5.321 55.821 3016 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.14 % Favored : 91.83 % Rotamer: Outliers : 1.77 % Allowed : 15.43 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2728 helix: 0.62 (0.16), residues: 1170 sheet: -0.25 (0.28), residues: 346 loop : -1.42 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1054 TYR 0.016 0.002 TYR C 503 PHE 0.022 0.002 PHE C1078 TRP 0.016 0.002 TRP A 624 HIS 0.007 0.001 HIS C 875 Details of bonding type rmsd covalent geometry : bond 0.00467 (21556) covalent geometry : angle 0.73135 (29220) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.87865 ( 8) hydrogen bonds : bond 0.03730 ( 882) hydrogen bonds : angle 5.79536 ( 2601) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.812 Fit side-chains REVERT: A 508 MET cc_start: 0.9523 (mmp) cc_final: 0.9037 (mmp) REVERT: A 690 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: A 900 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7985 (mmt) REVERT: A 921 MET cc_start: 0.7847 (ptt) cc_final: 0.7496 (ppp) REVERT: A 1106 LYS cc_start: 0.9619 (tptp) cc_final: 0.9352 (mmmt) REVERT: A 1153 MET cc_start: 0.8407 (ppp) cc_final: 0.7767 (ppp) REVERT: A 1166 MET cc_start: 0.8570 (ptp) cc_final: 0.8123 (pmm) REVERT: B 508 MET cc_start: 0.9165 (mmp) cc_final: 0.8904 (mmp) REVERT: B 566 MET cc_start: 0.8104 (tpp) cc_final: 0.7809 (tpp) REVERT: B 616 MET cc_start: 0.7972 (mmp) cc_final: 0.7741 (mmp) REVERT: B 671 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7127 (tpp) REVERT: B 934 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: B 959 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5983 (p90) REVERT: B 1012 MET cc_start: 0.8304 (pmm) cc_final: 0.7981 (pmm) REVERT: B 1116 MET cc_start: 0.7833 (mmt) cc_final: 0.6837 (ptm) REVERT: B 1145 MET cc_start: 0.6471 (ptt) cc_final: 0.6068 (ptt) REVERT: C 754 MET cc_start: 0.9444 (ppp) cc_final: 0.9201 (ppp) REVERT: C 783 MET cc_start: 0.9078 (tpp) cc_final: 0.8809 (tmm) REVERT: C 804 MET cc_start: 0.8539 (tpp) cc_final: 0.8136 (tpp) REVERT: D 566 MET cc_start: 0.4237 (tpp) cc_final: 0.3748 (tpt) REVERT: D 604 MET cc_start: 0.8178 (tpt) cc_final: 0.7969 (tpp) REVERT: D 706 TYR cc_start: 0.6950 (t80) cc_final: 0.6611 (t80) REVERT: D 810 MET cc_start: 0.9096 (mmp) cc_final: 0.8635 (mmm) REVERT: D 881 MET cc_start: 0.9480 (mmp) cc_final: 0.9187 (mmm) outliers start: 40 outliers final: 22 residues processed: 176 average time/residue: 0.1282 time to fit residues: 37.2796 Evaluate side-chains 170 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 142 optimal weight: 0.0170 chunk 271 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 61 optimal weight: 0.0270 chunk 96 optimal weight: 5.9990 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 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 = 0.3495 r_free = 0.3495 target = 0.045031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.033276 restraints weight = 234853.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.033912 restraints weight = 182643.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.034351 restraints weight = 151419.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034712 restraints weight = 132102.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.034953 restraints weight = 119209.153| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21565 Z= 0.126 Angle : 0.685 11.919 29228 Z= 0.331 Chirality : 0.043 0.283 3264 Planarity : 0.004 0.039 3828 Dihedral : 5.215 58.446 3016 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.07 % Favored : 92.89 % Rotamer: Outliers : 1.42 % Allowed : 16.40 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2728 helix: 0.74 (0.16), residues: 1170 sheet: -0.15 (0.28), residues: 346 loop : -1.43 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1054 TYR 0.012 0.001 TYR C 837 PHE 0.011 0.001 PHE C1077 TRP 0.012 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00278 (21556) covalent geometry : angle 0.68521 (29220) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.98810 ( 8) hydrogen bonds : bond 0.03346 ( 882) hydrogen bonds : angle 5.54975 ( 2601) Misc. bond : bond 0.00024 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9520 (mmp) cc_final: 0.9024 (mmp) REVERT: A 690 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7622 (mmm) REVERT: A 804 MET cc_start: 0.8601 (tpp) cc_final: 0.8198 (mmm) REVERT: A 854 MET cc_start: 0.6202 (tmm) cc_final: 0.5474 (tmm) REVERT: A 921 MET cc_start: 0.7748 (ptt) cc_final: 0.7405 (ppp) REVERT: A 1106 LYS cc_start: 0.9607 (tptp) cc_final: 0.9317 (mmmt) REVERT: A 1153 MET cc_start: 0.8283 (ppp) cc_final: 0.7720 (ppp) REVERT: A 1166 MET cc_start: 0.8568 (ptp) cc_final: 0.8106 (pmm) REVERT: B 508 MET cc_start: 0.9051 (mmp) cc_final: 0.8798 (mmp) REVERT: B 566 MET cc_start: 0.8054 (tpp) cc_final: 0.7810 (tpp) REVERT: B 616 MET cc_start: 0.7770 (mmp) cc_final: 0.7552 (mmp) REVERT: B 671 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7048 (tpp) REVERT: B 934 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: B 959 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5875 (p90) REVERT: B 1078 PHE cc_start: 0.9011 (m-80) cc_final: 0.8349 (t80) REVERT: B 1116 MET cc_start: 0.7658 (mmt) cc_final: 0.6767 (ptm) REVERT: B 1145 MET cc_start: 0.6410 (ptt) cc_final: 0.5908 (ptt) REVERT: C 508 MET cc_start: 0.8932 (mmt) cc_final: 0.8235 (mmt) REVERT: C 754 MET cc_start: 0.9445 (ppp) cc_final: 0.9217 (ppp) REVERT: C 783 MET cc_start: 0.9085 (tpp) cc_final: 0.8817 (tmm) REVERT: C 804 MET cc_start: 0.8451 (tpp) cc_final: 0.8133 (tpp) REVERT: D 604 MET cc_start: 0.8223 (tpt) cc_final: 0.7854 (tpp) REVERT: D 706 TYR cc_start: 0.6875 (t80) cc_final: 0.6113 (t80) REVERT: D 746 LEU cc_start: 0.9265 (mt) cc_final: 0.8756 (pt) REVERT: D 810 MET cc_start: 0.9102 (mmp) cc_final: 0.8625 (mmm) REVERT: D 854 MET cc_start: 0.8282 (ttt) cc_final: 0.8001 (ttt) REVERT: D 881 MET cc_start: 0.9494 (mmp) cc_final: 0.9194 (mmm) outliers start: 32 outliers final: 23 residues processed: 168 average time/residue: 0.1262 time to fit residues: 35.3190 Evaluate side-chains 170 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 2 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 GLN B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 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 = 0.3504 r_free = 0.3504 target = 0.045393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.033481 restraints weight = 230723.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.034117 restraints weight = 179601.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.034572 restraints weight = 149112.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.034931 restraints weight = 129893.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.035075 restraints weight = 117350.159| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21565 Z= 0.117 Angle : 0.685 11.749 29228 Z= 0.329 Chirality : 0.043 0.310 3264 Planarity : 0.004 0.041 3828 Dihedral : 5.046 54.504 3016 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.18 % Favored : 92.78 % Rotamer: Outliers : 1.60 % Allowed : 16.13 % Favored : 82.27 % 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: -0.40 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1164 sheet: -0.12 (0.28), residues: 354 loop : -1.38 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1054 TYR 0.012 0.001 TYR B 837 PHE 0.024 0.001 PHE C1078 TRP 0.010 0.001 TRP D 607 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00261 (21556) covalent geometry : angle 0.68484 (29220) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.10798 ( 8) hydrogen bonds : bond 0.03284 ( 882) hydrogen bonds : angle 5.43534 ( 2601) Misc. bond : bond 0.00018 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.802 Fit side-chains REVERT: A 508 MET cc_start: 0.9516 (mmp) cc_final: 0.9094 (mmp) REVERT: A 690 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: A 804 MET cc_start: 0.8508 (tpp) cc_final: 0.8087 (mmm) REVERT: A 854 MET cc_start: 0.6042 (tmm) cc_final: 0.5281 (tmm) REVERT: A 921 MET cc_start: 0.7713 (ptt) cc_final: 0.7444 (ppp) REVERT: A 1106 LYS cc_start: 0.9602 (tptp) cc_final: 0.9338 (mmmt) REVERT: A 1153 MET cc_start: 0.8288 (ppp) cc_final: 0.7718 (ppp) REVERT: A 1166 MET cc_start: 0.8542 (ptp) cc_final: 0.8062 (pmm) REVERT: B 508 MET cc_start: 0.8999 (mmp) cc_final: 0.8754 (mmp) REVERT: B 616 MET cc_start: 0.7704 (mmp) cc_final: 0.7500 (mmp) REVERT: B 671 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6997 (tpp) REVERT: B 724 MET cc_start: 0.8792 (mmt) cc_final: 0.8530 (mmm) REVERT: B 934 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: B 959 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5890 (p90) REVERT: B 1116 MET cc_start: 0.7588 (mmt) cc_final: 0.6723 (ptm) REVERT: B 1145 MET cc_start: 0.6488 (ptt) cc_final: 0.6042 (ptt) REVERT: C 508 MET cc_start: 0.8892 (mmt) cc_final: 0.8152 (mmt) REVERT: C 783 MET cc_start: 0.9049 (tpp) cc_final: 0.8810 (tmm) REVERT: C 804 MET cc_start: 0.8469 (tpp) cc_final: 0.8146 (tpp) REVERT: D 604 MET cc_start: 0.8248 (tpt) cc_final: 0.7822 (tpp) REVERT: D 706 TYR cc_start: 0.7000 (t80) cc_final: 0.6252 (t80) REVERT: D 730 LEU cc_start: 0.8177 (tp) cc_final: 0.7954 (mm) REVERT: D 746 LEU cc_start: 0.9263 (mt) cc_final: 0.8801 (pt) REVERT: D 810 MET cc_start: 0.9053 (mmp) cc_final: 0.8587 (mmm) REVERT: D 854 MET cc_start: 0.8339 (ttt) cc_final: 0.8089 (ttt) REVERT: D 881 MET cc_start: 0.9524 (mmp) cc_final: 0.9204 (mmm) outliers start: 36 outliers final: 25 residues processed: 171 average time/residue: 0.1266 time to fit residues: 36.3832 Evaluate side-chains 170 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 222 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 192 optimal weight: 0.5980 chunk 267 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 202 optimal weight: 30.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 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 = 0.3498 r_free = 0.3498 target = 0.045181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.033466 restraints weight = 233987.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.034077 restraints weight = 184753.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.034521 restraints weight = 152307.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.034871 restraints weight = 132128.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.035089 restraints weight = 118716.364| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21565 Z= 0.127 Angle : 0.718 14.270 29228 Z= 0.341 Chirality : 0.043 0.288 3264 Planarity : 0.004 0.048 3828 Dihedral : 5.032 53.057 3016 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.00 % Favored : 92.96 % Rotamer: Outliers : 1.29 % Allowed : 16.80 % Favored : 81.91 % 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: -0.38 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1162 sheet: -0.10 (0.29), residues: 350 loop : -1.35 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.012 0.001 TYR B 837 PHE 0.011 0.001 PHE C1077 TRP 0.008 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00281 (21556) covalent geometry : angle 0.71756 (29220) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.95162 ( 8) hydrogen bonds : bond 0.03291 ( 882) hydrogen bonds : angle 5.46864 ( 2601) Misc. bond : bond 0.00020 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9515 (mmp) cc_final: 0.9053 (mmp) REVERT: A 690 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7664 (mmm) REVERT: A 804 MET cc_start: 0.8475 (tpp) cc_final: 0.7978 (mmm) REVERT: A 854 MET cc_start: 0.5912 (tmm) cc_final: 0.5119 (tmm) REVERT: A 921 MET cc_start: 0.7736 (ptt) cc_final: 0.7318 (ppp) REVERT: A 1106 LYS cc_start: 0.9611 (tptp) cc_final: 0.9345 (mmmt) REVERT: A 1153 MET cc_start: 0.8280 (ppp) cc_final: 0.7703 (ppp) REVERT: A 1166 MET cc_start: 0.8577 (ptp) cc_final: 0.8082 (pmm) REVERT: B 508 MET cc_start: 0.9009 (mmp) cc_final: 0.8787 (mmp) REVERT: B 671 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7005 (tpp) REVERT: B 724 MET cc_start: 0.8708 (mmt) cc_final: 0.8499 (mmm) REVERT: B 810 MET cc_start: 0.9309 (mmm) cc_final: 0.9091 (mmt) REVERT: B 934 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: B 959 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5987 (p90) REVERT: B 1078 PHE cc_start: 0.9019 (m-80) cc_final: 0.8348 (t80) REVERT: B 1116 MET cc_start: 0.7584 (mmt) cc_final: 0.6720 (ptm) REVERT: B 1145 MET cc_start: 0.6421 (ptt) cc_final: 0.5939 (ptt) REVERT: C 508 MET cc_start: 0.8904 (mmt) cc_final: 0.8161 (mmt) REVERT: C 783 MET cc_start: 0.9021 (tpp) cc_final: 0.8785 (tmm) REVERT: C 804 MET cc_start: 0.8543 (tpp) cc_final: 0.8212 (tpp) REVERT: D 604 MET cc_start: 0.8175 (tpt) cc_final: 0.7769 (tpp) REVERT: D 706 TYR cc_start: 0.7128 (t80) cc_final: 0.6353 (t80) REVERT: D 730 LEU cc_start: 0.8139 (tp) cc_final: 0.7921 (mm) REVERT: D 746 LEU cc_start: 0.9236 (mt) cc_final: 0.8845 (pt) REVERT: D 810 MET cc_start: 0.9062 (mmp) cc_final: 0.8603 (mmm) REVERT: D 854 MET cc_start: 0.8355 (ttt) cc_final: 0.8087 (ttt) REVERT: D 881 MET cc_start: 0.9546 (mmp) cc_final: 0.9215 (mmm) outliers start: 29 outliers final: 24 residues processed: 162 average time/residue: 0.1248 time to fit residues: 34.1366 Evaluate side-chains 168 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 934 GLN Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 722 TYR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.045399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.033503 restraints weight = 232926.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.034121 restraints weight = 179818.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.034588 restraints weight = 148803.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.034952 restraints weight = 129300.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.035179 restraints weight = 116041.187| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21565 Z= 0.120 Angle : 0.708 12.236 29228 Z= 0.336 Chirality : 0.043 0.273 3264 Planarity : 0.004 0.043 3828 Dihedral : 4.966 52.985 3016 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.00 % Favored : 92.96 % Rotamer: Outliers : 1.20 % Allowed : 16.84 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1164 sheet: -0.03 (0.29), residues: 346 loop : -1.36 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.011 0.001 TYR B 837 PHE 0.024 0.001 PHE C1078 TRP 0.008 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00266 (21556) covalent geometry : angle 0.70810 (29220) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.99847 ( 8) hydrogen bonds : bond 0.03218 ( 882) hydrogen bonds : angle 5.39235 ( 2601) Misc. bond : bond 0.00021 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.11 seconds wall clock time: 65 minutes 6.87 seconds (3906.87 seconds total)