Starting phenix.real_space_refine on Fri Mar 6 13:58:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqv_23489/03_2026/7lqv_23489.cif" } resolution = 3.25 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= -0.001 sd= 0.040 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 144 5.16 5 C 19854 2.51 5 N 5185 2.21 5 O 6091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 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: 31274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8535 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 55, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8681 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 55, 'TRANS': 1056} Chain breaks: 3 Chain: "C" Number of atoms: 8500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8500 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 55, 'TRANS': 1031} Chain breaks: 4 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "W" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "X" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 775 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "Y" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Z" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.63, per 1000 atoms: 0.24 Number of scatterers: 31274 At special positions: 0 Unit cell: (198.904, 186.208, 203.136, 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 144 16.00 O 6091 8.00 N 5185 7.00 C 19854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1306 " - " ASN A 603 " " NAG A1309 " - " ASN A 709 " " NAG B1303 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 65 sheets defined 20.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.855A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.681A pdb=" N HIS A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.602A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.769A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.786A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.577A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.174A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.666A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.839A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.637A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.823A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.850A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.519A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.764A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.506A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 855' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.891A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.386A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.615A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.283A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.641A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.031A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.980A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.614A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.934A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.781A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.978A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 removed outlier: 3.712A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 856' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.859A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.318A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.524A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.401A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.964A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.774A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 4.037A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 100B through 100F removed outlier: 3.515A pdb=" N TYR H 100F" --> pdb=" O GLU H 100C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.753A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 100B through 100F Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.751A pdb=" N GLU X 83 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100B through 100F Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.607A pdb=" N GLU Z 83 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.549A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.631A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.148A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.147A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 224 through 229 removed outlier: 5.446A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.548A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.615A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.553A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.791A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.328A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.562A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.629A pdb=" N HIS B 69 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.945A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.997A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.408A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.508A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 374 through 379 removed outlier: 4.543A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.531A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.331A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.410A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.646A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 78 " --> pdb=" O HIS C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.214A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.794A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 225 through 229 removed outlier: 5.384A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.653A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 653 through 655 removed outlier: 5.953A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.853A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.717A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.643A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.914A pdb=" N ALA L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 97 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.626A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 5 through 6 removed outlier: 3.975A pdb=" N VAL W 20 " --> pdb=" O MET W 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET W 80 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA W 78 " --> pdb=" O CYS W 22 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP W 72 " --> pdb=" O THR W 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 13 removed outlier: 6.604A pdb=" N GLU W 10 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER W 112 " --> pdb=" O GLU W 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS W 12 " --> pdb=" O SER W 112 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR W 90 " --> pdb=" O THR W 107 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE W 34 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG W 50 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET W 48 " --> pdb=" O TRP W 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 9 through 12 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 3.994A pdb=" N ALA X 90 " --> pdb=" O VAL X 97 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL X 97 " --> pdb=" O ALA X 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 19 through 24 removed outlier: 3.543A pdb=" N ALA X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 5 through 6 removed outlier: 3.851A pdb=" N VAL Y 20 " --> pdb=" O MET Y 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET Y 80 " --> pdb=" O VAL Y 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA Y 78 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP Y 72 " --> pdb=" O THR Y 77 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE Y 34 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG Y 50 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP Y 36 " --> pdb=" O MET Y 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL Y 102 " --> pdb=" O SER Y 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 9 through 13 Processing sheet with id=AH1, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.026A pdb=" N ALA Z 90 " --> pdb=" O VAL Z 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL Z 97 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 19 through 24 removed outlier: 3.578A pdb=" N ALA Z 19 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2817 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: 8.12 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7222 1.33 - 1.45: 7464 1.45 - 1.58: 17108 1.58 - 1.70: 1 1.70 - 1.83: 186 Bond restraints: 31981 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.52e-02 4.33e+03 1.84e+01 bond pdb=" CB ASN A1134 " pdb=" CG ASN A1134 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.90e+00 bond pdb=" N ASP A 53 " pdb=" CA ASP A 53 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.16e-02 7.43e+03 5.70e+00 bond pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N LYS A 814 " pdb=" CA LYS A 814 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.12e-02 7.97e+03 5.33e+00 ... (remaining 31976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 42144 1.33 - 2.65: 1047 2.65 - 3.98: 259 3.98 - 5.31: 71 5.31 - 6.63: 11 Bond angle restraints: 43532 Sorted by residual: angle pdb=" CA ARG A 815 " pdb=" C ARG A 815 " pdb=" O ARG A 815 " ideal model delta sigma weight residual 121.88 116.39 5.49 1.13e+00 7.83e-01 2.36e+01 angle pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 121.19 116.49 4.70 1.10e+00 8.26e-01 1.83e+01 angle pdb=" N ALA A 522 " pdb=" CA ALA A 522 " pdb=" C ALA A 522 " ideal model delta sigma weight residual 107.73 113.94 -6.21 1.61e+00 3.86e-01 1.49e+01 angle pdb=" CA ASP A 53 " pdb=" C ASP A 53 " pdb=" O ASP A 53 " ideal model delta sigma weight residual 121.38 117.51 3.87 1.06e+00 8.90e-01 1.34e+01 angle pdb=" C THR A 51 " pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta sigma weight residual 110.62 105.31 5.31 1.51e+00 4.39e-01 1.24e+01 ... (remaining 43527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 17938 20.84 - 41.68: 1216 41.68 - 62.52: 189 62.52 - 83.37: 43 83.37 - 104.21: 22 Dihedral angle restraints: 19408 sinusoidal: 7860 harmonic: 11548 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -167.85 81.85 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 26.68 66.32 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 19405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3782 0.040 - 0.080: 729 0.080 - 0.120: 414 0.120 - 0.160: 60 0.160 - 0.200: 8 Chirality restraints: 4993 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU A 821 " pdb=" N LEU A 821 " pdb=" C LEU A 821 " pdb=" CB LEU A 821 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 4990 not shown) Planarity restraints: 5594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A1106 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" CD GLN A1106 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1106 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1106 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C1089 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C1090 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C1090 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C1090 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 54 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEU A 54 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 54 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 55 " -0.011 2.00e-02 2.50e+03 ... (remaining 5591 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 363 2.60 - 3.17: 27614 3.17 - 3.75: 45904 3.75 - 4.32: 64638 4.32 - 4.90: 107725 Nonbonded interactions: 246244 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" O ALA A 522 " model vdw 2.020 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.040 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.067 3.040 nonbonded pdb=" OG SER B 816 " pdb=" OE1 GLU B 819 " model vdw 2.089 3.040 nonbonded pdb=" OE2 GLU C 654 " pdb=" OG SER C 691 " model vdw 2.098 3.040 ... (remaining 246239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 827 or resid 853 through 1308)) selection = (chain 'B' and (resid 14 through 827 or resid 853 through 1308)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'L' and (resid 2 through 49 or resid 51 through 106A)) selection = chain 'X' selection = (chain 'Z' and (resid 2 through 49 or resid 51 through 106A)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.710 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.003 0.066 32034 Z= 0.151 Angle : 0.568 14.226 43642 Z= 0.299 Chirality : 0.043 0.200 4993 Planarity : 0.003 0.049 5590 Dihedral : 13.962 104.206 11853 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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 (0.14), residues: 3938 helix: 1.82 (0.22), residues: 607 sheet: 0.08 (0.18), residues: 809 loop : -0.96 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.025 0.001 TYR C 508 PHE 0.015 0.001 PHE C 759 TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00307 (31981) covalent geometry : angle 0.55645 (43532) SS BOND : bond 0.00317 ( 49) SS BOND : angle 1.05311 ( 98) hydrogen bonds : bond 0.25207 ( 1025) hydrogen bonds : angle 9.32726 ( 2817) link_NAG-ASN : bond 0.00990 ( 4) link_NAG-ASN : angle 6.40361 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.7560 (m-40) cc_final: 0.7339 (m-40) REVERT: C 1002 GLN cc_start: 0.8673 (tt0) cc_final: 0.8219 (tp-100) REVERT: W 100 TYR cc_start: 0.5571 (m-80) cc_final: 0.5237 (m-80) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.1801 time to fit residues: 58.1536 Evaluate side-chains 133 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 901 GLN A1134 ASN B 804 GLN B1134 ASN C 935 GLN H 1 GLN H 39 GLN L 38 GLN L 50 GLN W 39 GLN Y 39 GLN Z 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.153991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099839 restraints weight = 83343.201| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.57 r_work: 0.3332 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32034 Z= 0.150 Angle : 0.600 9.033 43642 Z= 0.313 Chirality : 0.046 0.292 4993 Planarity : 0.004 0.047 5590 Dihedral : 6.849 73.947 4862 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.34 % Rotamer: Outliers : 0.38 % Allowed : 5.38 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.43 (0.13), residues: 3938 helix: 1.75 (0.21), residues: 618 sheet: 0.13 (0.18), residues: 823 loop : -1.00 (0.13), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.022 0.001 TYR C1067 PHE 0.029 0.001 PHE A 168 TRP 0.017 0.002 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00329 (31981) covalent geometry : angle 0.59238 (43532) SS BOND : bond 0.00388 ( 49) SS BOND : angle 1.55566 ( 98) hydrogen bonds : bond 0.04693 ( 1025) hydrogen bonds : angle 6.67004 ( 2817) link_NAG-ASN : bond 0.00968 ( 4) link_NAG-ASN : angle 4.05327 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8777 (m-30) cc_final: 0.8554 (p0) REVERT: A 200 TYR cc_start: 0.7549 (m-80) cc_final: 0.7038 (m-80) REVERT: A 904 TYR cc_start: 0.7838 (t80) cc_final: 0.7529 (t80) REVERT: B 64 TRP cc_start: 0.8819 (t60) cc_final: 0.8588 (t60) REVERT: C 394 ASN cc_start: 0.8090 (m-40) cc_final: 0.7763 (t0) REVERT: C 697 MET cc_start: 0.8430 (ptp) cc_final: 0.8203 (ptm) REVERT: C 1002 GLN cc_start: 0.8990 (tt0) cc_final: 0.8410 (tp-100) REVERT: W 100 ILE cc_start: 0.5369 (mm) cc_final: 0.4609 (tt) REVERT: W 100 TYR cc_start: 0.5455 (m-80) cc_final: 0.4598 (m-80) REVERT: Z 24 SER cc_start: 0.6152 (p) cc_final: 0.5847 (t) outliers start: 13 outliers final: 6 residues processed: 176 average time/residue: 0.1685 time to fit residues: 51.5937 Evaluate side-chains 140 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain Z residue 50 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 146 optimal weight: 1.9990 chunk 339 optimal weight: 40.0000 chunk 333 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 394 ASN A 853 GLN A 957 GLN B 282 ASN B 762 GLN B 764 ASN B 955 ASN C 121 ASN C 709 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN X 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.154181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099991 restraints weight = 83956.085| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.49 r_work: 0.3285 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32034 Z= 0.162 Angle : 0.564 9.373 43642 Z= 0.292 Chirality : 0.044 0.294 4993 Planarity : 0.004 0.048 5590 Dihedral : 5.948 57.283 4858 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.81 % Allowed : 7.56 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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 (0.13), residues: 3938 helix: 1.55 (0.21), residues: 635 sheet: 0.10 (0.17), residues: 834 loop : -1.07 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 214 TYR 0.022 0.001 TYR B 28 PHE 0.027 0.001 PHE A 65 TRP 0.012 0.001 TRP Y 103 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00370 (31981) covalent geometry : angle 0.55612 (43532) SS BOND : bond 0.00550 ( 49) SS BOND : angle 1.57953 ( 98) hydrogen bonds : bond 0.04218 ( 1025) hydrogen bonds : angle 6.23715 ( 2817) link_NAG-ASN : bond 0.00830 ( 4) link_NAG-ASN : angle 3.56046 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7723 (m-10) cc_final: 0.7399 (m-80) REVERT: A 780 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: A 904 TYR cc_start: 0.8035 (t80) cc_final: 0.7713 (t80) REVERT: C 104 TRP cc_start: 0.7252 (m-90) cc_final: 0.6793 (m-90) REVERT: C 394 ASN cc_start: 0.8046 (m-40) cc_final: 0.7703 (t0) REVERT: C 740 MET cc_start: 0.8433 (ttt) cc_final: 0.8228 (ttm) REVERT: C 1002 GLN cc_start: 0.9039 (tt0) cc_final: 0.8477 (tp-100) REVERT: H 48 MET cc_start: -0.1109 (tmm) cc_final: -0.1537 (ptt) REVERT: W 100 ILE cc_start: 0.5735 (mm) cc_final: 0.4987 (tt) REVERT: W 100 TYR cc_start: 0.5335 (m-80) cc_final: 0.4611 (m-10) REVERT: Z 24 SER cc_start: 0.6053 (p) cc_final: 0.5789 (t) outliers start: 28 outliers final: 15 residues processed: 175 average time/residue: 0.1608 time to fit residues: 49.8388 Evaluate side-chains 151 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 189 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 224 optimal weight: 0.0670 chunk 370 optimal weight: 30.0000 chunk 200 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 331 optimal weight: 20.0000 chunk 281 optimal weight: 0.1980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 935 GLN Z 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.154393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100266 restraints weight = 83034.850| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.61 r_work: 0.3307 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32034 Z= 0.110 Angle : 0.534 9.566 43642 Z= 0.276 Chirality : 0.043 0.296 4993 Planarity : 0.004 0.052 5590 Dihedral : 5.292 59.971 4858 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 0.87 % Allowed : 9.30 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3938 helix: 1.69 (0.21), residues: 638 sheet: 0.15 (0.18), residues: 831 loop : -1.03 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 38 TYR 0.026 0.001 TYR B 28 PHE 0.018 0.001 PHE B 65 TRP 0.017 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00243 (31981) covalent geometry : angle 0.52802 (43532) SS BOND : bond 0.00342 ( 49) SS BOND : angle 1.33165 ( 98) hydrogen bonds : bond 0.03566 ( 1025) hydrogen bonds : angle 5.84824 ( 2817) link_NAG-ASN : bond 0.00804 ( 4) link_NAG-ASN : angle 3.17768 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8841 (m-80) cc_final: 0.8520 (m-80) REVERT: A 88 ASP cc_start: 0.8853 (m-30) cc_final: 0.8521 (p0) REVERT: A 200 TYR cc_start: 0.7717 (m-10) cc_final: 0.6824 (m-80) REVERT: A 780 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: A 904 TYR cc_start: 0.8029 (t80) cc_final: 0.7697 (t80) REVERT: B 314 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8533 (tm-30) REVERT: C 104 TRP cc_start: 0.7364 (m-90) cc_final: 0.6990 (m-90) REVERT: C 394 ASN cc_start: 0.7972 (m-40) cc_final: 0.7458 (t0) REVERT: C 418 ILE cc_start: 0.8357 (pt) cc_final: 0.8134 (pt) REVERT: C 697 MET cc_start: 0.8461 (ptp) cc_final: 0.8208 (ptm) REVERT: C 935 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8181 (pp30) REVERT: C 1002 GLN cc_start: 0.9061 (tt0) cc_final: 0.8358 (tp-100) REVERT: H 48 MET cc_start: -0.1647 (tmm) cc_final: -0.1956 (ptm) REVERT: W 100 ILE cc_start: 0.5667 (mm) cc_final: 0.5026 (tt) REVERT: W 100 TYR cc_start: 0.5385 (m-80) cc_final: 0.4418 (m-10) REVERT: Z 24 SER cc_start: 0.6079 (p) cc_final: 0.5798 (t) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 0.1681 time to fit residues: 55.3812 Evaluate side-chains 150 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 223 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 373 optimal weight: 0.3980 chunk 187 optimal weight: 0.5980 chunk 270 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 200 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN B 955 ASN C 519 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.152070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096380 restraints weight = 76474.787| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.26 r_work: 0.3326 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32034 Z= 0.106 Angle : 0.525 9.568 43642 Z= 0.270 Chirality : 0.043 0.297 4993 Planarity : 0.004 0.052 5590 Dihedral : 4.886 55.767 4858 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 1.22 % Allowed : 10.23 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.42 (0.13), residues: 3938 helix: 1.73 (0.21), residues: 640 sheet: 0.07 (0.17), residues: 853 loop : -0.99 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.042 0.001 TYR B 28 PHE 0.020 0.001 PHE A 823 TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00240 (31981) covalent geometry : angle 0.51873 (43532) SS BOND : bond 0.00324 ( 49) SS BOND : angle 1.36711 ( 98) hydrogen bonds : bond 0.03436 ( 1025) hydrogen bonds : angle 5.68039 ( 2817) link_NAG-ASN : bond 0.00757 ( 4) link_NAG-ASN : angle 3.06558 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8845 (m-80) cc_final: 0.8520 (m-80) REVERT: A 88 ASP cc_start: 0.8801 (m-30) cc_final: 0.8571 (p0) REVERT: A 200 TYR cc_start: 0.7758 (m-10) cc_final: 0.7402 (m-10) REVERT: A 780 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: A 904 TYR cc_start: 0.7956 (t80) cc_final: 0.7723 (t80) REVERT: B 314 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 425 LEU cc_start: 0.0075 (OUTLIER) cc_final: -0.0571 (mt) REVERT: C 394 ASN cc_start: 0.7914 (m-40) cc_final: 0.7554 (t0) REVERT: C 408 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8320 (ttp80) REVERT: C 780 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: C 1002 GLN cc_start: 0.9020 (tt0) cc_final: 0.8394 (tp-100) REVERT: W 100 ILE cc_start: 0.5470 (mm) cc_final: 0.4930 (tt) REVERT: W 100 TYR cc_start: 0.5458 (m-80) cc_final: 0.4555 (m-10) outliers start: 42 outliers final: 19 residues processed: 175 average time/residue: 0.1652 time to fit residues: 50.3993 Evaluate side-chains 149 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 156 optimal weight: 20.0000 chunk 362 optimal weight: 0.2980 chunk 168 optimal weight: 0.0570 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 340 optimal weight: 0.0070 chunk 63 optimal weight: 0.9980 chunk 289 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 955 ASN C 519 HIS W 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.147275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095235 restraints weight = 82490.011| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.42 r_work: 0.3333 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32034 Z= 0.098 Angle : 0.513 9.575 43642 Z= 0.263 Chirality : 0.043 0.297 4993 Planarity : 0.004 0.053 5590 Dihedral : 4.519 55.820 4858 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.25 % Allowed : 11.08 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.35 (0.13), residues: 3938 helix: 1.79 (0.21), residues: 646 sheet: 0.12 (0.17), residues: 840 loop : -0.96 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.024 0.001 TYR B 28 PHE 0.015 0.001 PHE C 374 TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00217 (31981) covalent geometry : angle 0.50917 (43532) SS BOND : bond 0.00252 ( 49) SS BOND : angle 1.05707 ( 98) hydrogen bonds : bond 0.03234 ( 1025) hydrogen bonds : angle 5.46628 ( 2817) link_NAG-ASN : bond 0.00759 ( 4) link_NAG-ASN : angle 2.98553 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8784 (m-80) cc_final: 0.8548 (m-80) REVERT: A 88 ASP cc_start: 0.8801 (m-30) cc_final: 0.8537 (p0) REVERT: A 200 TYR cc_start: 0.7783 (m-10) cc_final: 0.7417 (m-10) REVERT: A 780 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: A 904 TYR cc_start: 0.7909 (t80) cc_final: 0.7675 (t80) REVERT: B 314 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 425 LEU cc_start: 0.0132 (OUTLIER) cc_final: -0.0526 (mt) REVERT: B 902 MET cc_start: 0.9004 (tpt) cc_final: 0.8764 (tpt) REVERT: C 157 PHE cc_start: 0.7802 (m-10) cc_final: 0.7493 (m-10) REVERT: C 392 PHE cc_start: 0.7678 (m-80) cc_final: 0.7292 (m-10) REVERT: C 394 ASN cc_start: 0.7833 (m-40) cc_final: 0.7510 (t0) REVERT: C 408 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8376 (ttp80) REVERT: C 597 VAL cc_start: 0.8631 (m) cc_final: 0.8386 (m) REVERT: C 780 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: C 1002 GLN cc_start: 0.9011 (tt0) cc_final: 0.8390 (tp-100) REVERT: W 100 ILE cc_start: 0.5634 (mm) cc_final: 0.5017 (tt) REVERT: W 100 TYR cc_start: 0.5430 (m-80) cc_final: 0.4450 (m-10) outliers start: 43 outliers final: 22 residues processed: 178 average time/residue: 0.1692 time to fit residues: 53.1720 Evaluate side-chains 160 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 230 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 359 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 100 optimal weight: 0.6980 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 955 ASN B1058 HIS B1074 ASN C 218 GLN C 544 ASN C 606 ASN C 709 ASN C1074 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.147270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091947 restraints weight = 84858.058| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.36 r_work: 0.3186 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32034 Z= 0.182 Angle : 0.554 9.439 43642 Z= 0.284 Chirality : 0.044 0.297 4993 Planarity : 0.004 0.054 5590 Dihedral : 4.469 55.873 4858 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 1.34 % Allowed : 11.69 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.43 (0.13), residues: 3938 helix: 1.80 (0.21), residues: 629 sheet: -0.03 (0.17), residues: 849 loop : -0.97 (0.13), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.022 0.001 TYR C 904 PHE 0.018 0.001 PHE C 133 TRP 0.010 0.001 TRP Y 103 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00421 (31981) covalent geometry : angle 0.54930 (43532) SS BOND : bond 0.00359 ( 49) SS BOND : angle 1.31791 ( 98) hydrogen bonds : bond 0.03525 ( 1025) hydrogen bonds : angle 5.51076 ( 2817) link_NAG-ASN : bond 0.00719 ( 4) link_NAG-ASN : angle 2.98278 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8773 (m-80) cc_final: 0.8496 (m-80) REVERT: A 200 TYR cc_start: 0.7934 (m-10) cc_final: 0.7509 (m-10) REVERT: A 780 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: A 904 TYR cc_start: 0.8304 (t80) cc_final: 0.7973 (t80) REVERT: B 425 LEU cc_start: 0.0115 (OUTLIER) cc_final: -0.0529 (mt) REVERT: B 990 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8518 (mt-10) REVERT: C 394 ASN cc_start: 0.8104 (m-40) cc_final: 0.7717 (t0) REVERT: C 408 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8485 (ttp80) REVERT: C 780 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: C 990 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: C 1002 GLN cc_start: 0.9137 (tt0) cc_final: 0.8484 (tp-100) REVERT: W 100 ILE cc_start: 0.5439 (mm) cc_final: 0.4822 (tt) REVERT: W 100 TYR cc_start: 0.5275 (m-80) cc_final: 0.4306 (m-10) outliers start: 46 outliers final: 33 residues processed: 169 average time/residue: 0.1670 time to fit residues: 49.2847 Evaluate side-chains 164 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 301 optimal weight: 0.6980 chunk 391 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.145828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.089654 restraints weight = 82760.028| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.09 r_work: 0.3288 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32034 Z= 0.106 Angle : 0.516 9.545 43642 Z= 0.265 Chirality : 0.043 0.291 4993 Planarity : 0.004 0.063 5590 Dihedral : 4.304 55.921 4858 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 1.02 % Allowed : 12.21 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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 (0.13), residues: 3938 helix: 1.78 (0.21), residues: 640 sheet: 0.15 (0.18), residues: 795 loop : -0.97 (0.13), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.029 0.001 TYR B 904 PHE 0.013 0.001 PHE C1121 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00238 (31981) covalent geometry : angle 0.51216 (43532) SS BOND : bond 0.00262 ( 49) SS BOND : angle 1.06365 ( 98) hydrogen bonds : bond 0.03209 ( 1025) hydrogen bonds : angle 5.37267 ( 2817) link_NAG-ASN : bond 0.00736 ( 4) link_NAG-ASN : angle 2.90574 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8804 (m-80) cc_final: 0.8600 (m-80) REVERT: A 88 ASP cc_start: 0.8837 (m-30) cc_final: 0.8435 (p0) REVERT: A 200 TYR cc_start: 0.7880 (m-10) cc_final: 0.7547 (m-80) REVERT: A 780 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: A 904 TYR cc_start: 0.8023 (t80) cc_final: 0.7791 (t80) REVERT: B 425 LEU cc_start: 0.0146 (OUTLIER) cc_final: -0.0488 (mt) REVERT: C 394 ASN cc_start: 0.7938 (m-40) cc_final: 0.7621 (t0) REVERT: C 408 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8186 (ptm-80) REVERT: C 780 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 990 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: C 1002 GLN cc_start: 0.9028 (tt0) cc_final: 0.8436 (tp-100) REVERT: W 100 ILE cc_start: 0.5143 (mm) cc_final: 0.4617 (tt) REVERT: W 100 TYR cc_start: 0.5479 (m-80) cc_final: 0.4435 (m-10) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.1671 time to fit residues: 49.4866 Evaluate side-chains 161 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 81 optimal weight: 0.9980 chunk 300 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 366 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 289 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 422 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 = 0.4467 r_free = 0.4467 target = 0.145489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088997 restraints weight = 82922.805| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.16 r_work: 0.3284 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32034 Z= 0.119 Angle : 0.520 9.512 43642 Z= 0.266 Chirality : 0.043 0.294 4993 Planarity : 0.004 0.054 5590 Dihedral : 4.251 55.982 4858 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 1.05 % Allowed : 12.53 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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 (0.13), residues: 3938 helix: 1.87 (0.21), residues: 635 sheet: 0.10 (0.18), residues: 788 loop : -0.97 (0.13), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 646 TYR 0.023 0.001 TYR C 28 PHE 0.013 0.001 PHE C1121 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (31981) covalent geometry : angle 0.51605 (43532) SS BOND : bond 0.00276 ( 49) SS BOND : angle 1.10557 ( 98) hydrogen bonds : bond 0.03220 ( 1025) hydrogen bonds : angle 5.28611 ( 2817) link_NAG-ASN : bond 0.00717 ( 4) link_NAG-ASN : angle 2.90916 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8806 (m-80) cc_final: 0.8585 (m-80) REVERT: A 88 ASP cc_start: 0.8835 (m-30) cc_final: 0.8434 (p0) REVERT: A 200 TYR cc_start: 0.7897 (m-10) cc_final: 0.7571 (m-80) REVERT: A 780 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 904 TYR cc_start: 0.7971 (t80) cc_final: 0.7752 (t80) REVERT: B 425 LEU cc_start: 0.0174 (OUTLIER) cc_final: -0.0480 (mt) REVERT: C 394 ASN cc_start: 0.7946 (m-40) cc_final: 0.7638 (t0) REVERT: C 408 ARG cc_start: 0.8742 (ttp80) cc_final: 0.8197 (ptm-80) REVERT: C 780 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 990 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: C 1002 GLN cc_start: 0.8997 (tt0) cc_final: 0.8411 (tp-100) REVERT: C 1050 MET cc_start: 0.8617 (ppp) cc_final: 0.8329 (ptm) REVERT: W 100 ILE cc_start: 0.5400 (mm) cc_final: 0.4865 (tt) REVERT: W 100 TYR cc_start: 0.5459 (m-80) cc_final: 0.4388 (m-10) outliers start: 36 outliers final: 28 residues processed: 167 average time/residue: 0.1641 time to fit residues: 48.2743 Evaluate side-chains 161 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 240 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 245 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.143843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089636 restraints weight = 83989.794| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.45 r_work: 0.3218 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32034 Z= 0.215 Angle : 0.587 9.345 43642 Z= 0.301 Chirality : 0.045 0.296 4993 Planarity : 0.004 0.091 5590 Dihedral : 4.482 56.025 4858 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.45 % Rotamer: Outliers : 1.10 % Allowed : 12.56 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.59 (0.13), residues: 3938 helix: 1.59 (0.21), residues: 633 sheet: -0.18 (0.18), residues: 823 loop : -1.03 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 646 TYR 0.031 0.001 TYR C 904 PHE 0.016 0.001 PHE B1089 TRP 0.012 0.001 TRP Y 36 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00498 (31981) covalent geometry : angle 0.58155 (43532) SS BOND : bond 0.00397 ( 49) SS BOND : angle 1.48830 ( 98) hydrogen bonds : bond 0.03620 ( 1025) hydrogen bonds : angle 5.45997 ( 2817) link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 2.95660 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8011 (m-10) cc_final: 0.7729 (m-10) REVERT: A 780 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: A 904 TYR cc_start: 0.8064 (t80) cc_final: 0.7735 (t80) REVERT: B 425 LEU cc_start: 0.0260 (OUTLIER) cc_final: -0.0427 (mt) REVERT: B 990 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8417 (mt-10) REVERT: C 408 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8310 (ptm-80) REVERT: C 990 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: C 1002 GLN cc_start: 0.9091 (tt0) cc_final: 0.8462 (tp-100) REVERT: W 100 ILE cc_start: 0.5288 (mm) cc_final: 0.4741 (tt) REVERT: W 100 TYR cc_start: 0.5486 (m-80) cc_final: 0.4295 (m-10) outliers start: 38 outliers final: 31 residues processed: 168 average time/residue: 0.1708 time to fit residues: 50.8733 Evaluate side-chains 157 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 130 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 355 optimal weight: 3.9990 chunk 148 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 373 optimal weight: 30.0000 chunk 322 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.144138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087358 restraints weight = 83068.593| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.20 r_work: 0.3230 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32034 Z= 0.137 Angle : 0.541 9.481 43642 Z= 0.276 Chirality : 0.043 0.290 4993 Planarity : 0.004 0.055 5590 Dihedral : 4.363 56.110 4858 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 1.19 % Allowed : 12.73 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.50 (0.13), residues: 3938 helix: 1.70 (0.21), residues: 635 sheet: -0.09 (0.18), residues: 799 loop : -0.99 (0.13), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.034 0.001 TYR B 904 PHE 0.023 0.001 PHE A 65 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00315 (31981) covalent geometry : angle 0.53650 (43532) SS BOND : bond 0.00307 ( 49) SS BOND : angle 1.25971 ( 98) hydrogen bonds : bond 0.03319 ( 1025) hydrogen bonds : angle 5.34203 ( 2817) link_NAG-ASN : bond 0.00711 ( 4) link_NAG-ASN : angle 2.89114 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11740.04 seconds wall clock time: 200 minutes 14.64 seconds (12014.64 seconds total)