Starting phenix.real_space_refine on Fri May 23 18:37:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.map" model { file = "/net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xki_38418/05_2025/8xki_38418.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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 102 5.16 5 C 15562 2.51 5 N 4016 2.21 5 O 4751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24431 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7599 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 51, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 7908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7908 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 53, 'TRANS': 963} Chain breaks: 7 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7548 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 51, 'TRANS': 938} Chain breaks: 9 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 116 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.20, per 1000 atoms: 0.66 Number of scatterers: 24431 At special positions: 0 Unit cell: (131.04, 141.96, 193.2, 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 102 16.00 O 4751 8.00 N 4016 7.00 C 15562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 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 BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG T 1 " - " NAG T 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG K 1 " - " ASN C1098 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG T 1 " - " ASN B1098 " " NAG W 1 " - " ASN B 717 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 3.3 seconds 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 57 sheets defined 23.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.627A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.722A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.056A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 760 through 774 Processing helix chain 'A' and resid 775 through 783 removed outlier: 3.994A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.881A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.907A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.319A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.679A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.631A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.857A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 990 through 1033 removed outlier: 3.770A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.794A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.716A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.086A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.661A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.798A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.518A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.355A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 4.326A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.791A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.736A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.690A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.698A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (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 removed outlier: 3.669A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 984 No H-bonds generated for 'chain 'B' and resid 983 through 984' Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.571A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.545A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.768A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.635A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 762 through 774 removed outlier: 3.950A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.601A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.730A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.505A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.756A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.609A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.553A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 954 " --> pdb=" O ASP C 950 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (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 990 through 1032 removed outlier: 3.559A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.520A pdb=" N CYS D 22 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.320A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.615A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.825A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.583A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 106 removed outlier: 4.091A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.893A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.461A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.891A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.565A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 572 through 573 removed outlier: 4.010A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.122A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.373A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AC1, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.764A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC3, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC6, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.537A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.619A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC9, first strand: chain 'B' and resid 101 through 107 removed outlier: 6.994A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.561A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.209A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.636A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.677A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.463A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.572A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.053A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.087A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 723 removed outlier: 6.902A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.561A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.726A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.893A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF1, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.159A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE C 392 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.536A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.105A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.737A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.737A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 769 hydrogen bonds defined for protein. 2067 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: 10.37 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7848 1.35 - 1.47: 6250 1.47 - 1.59: 10740 1.59 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 24968 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C CYS C 738 " pdb=" N THR C 739 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.38e-02 5.25e+03 5.13e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 24963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 33632 2.36 - 4.73: 362 4.73 - 7.09: 25 7.09 - 9.46: 2 9.46 - 11.82: 2 Bond angle restraints: 34023 Sorted by residual: angle pdb=" C THR C 333 " pdb=" N ASN C 334 " pdb=" CA ASN C 334 " ideal model delta sigma weight residual 121.90 116.20 5.70 1.26e+00 6.30e-01 2.05e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.07 -4.37 1.22e+00 6.72e-01 1.28e+01 angle pdb=" CA TYR A 170 " pdb=" CB TYR A 170 " pdb=" CG TYR A 170 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 angle pdb=" CA GLN B 493 " pdb=" CB GLN B 493 " pdb=" CG GLN B 493 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA VAL A 130 " pdb=" CB VAL A 130 " pdb=" CG1 VAL A 130 " ideal model delta sigma weight residual 110.40 115.99 -5.59 1.70e+00 3.46e-01 1.08e+01 ... (remaining 34018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 13787 24.81 - 49.61: 1173 49.61 - 74.42: 193 74.42 - 99.22: 56 99.22 - 124.03: 24 Dihedral angle restraints: 15233 sinusoidal: 6172 harmonic: 9061 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.73 -83.27 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -7.91 -78.09 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.60 -77.60 1 1.00e+01 1.00e-02 7.54e+01 ... (remaining 15230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3864 0.105 - 0.210: 127 0.210 - 0.314: 1 0.314 - 0.419: 0 0.419 - 0.524: 2 Chirality restraints: 3994 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3991 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 816 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 817 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 817 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 817 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.001 2.00e-02 2.50e+03 1.75e-02 3.81e+00 pdb=" CG ASN C 657 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 130 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C VAL A 130 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 130 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 131 " -0.011 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 852 2.70 - 3.25: 22449 3.25 - 3.80: 35313 3.80 - 4.35: 43424 4.35 - 4.90: 75679 Nonbonded interactions: 177717 Sorted by model distance: nonbonded pdb=" N GLU B 191 " pdb=" OE1 GLU B 191 " model vdw 2.156 3.120 nonbonded pdb=" NE2 GLN B 493 " pdb=" O SER B 494 " model vdw 2.201 3.120 nonbonded pdb=" OG SER C 803 " pdb=" O7 NAG C1307 " model vdw 2.224 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.230 3.120 nonbonded pdb=" O SER C 325 " pdb=" OG SER C 325 " model vdw 2.244 3.040 ... (remaining 177712 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 28 through 66 or (resid 80 through 81 and (name N or name \ CA or name C or name O or name CB )) or resid 82 through 108 or (resid 109 throu \ gh 111 and (name N or name CA or name C or name O or name CB )) or resid 112 thr \ ough 123 or (resid 124 through 125 and (name N or name CA or name C or name O or \ name CB )) or resid 126 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 196 or (resid 1 \ 97 through 198 and (name N or name CA or name C or name O or name CB )) or resid \ 199 through 205 or (resid 206 through 207 and (name N or name CA or name C or n \ ame O or name CB )) or resid 208 through 332 or (resid 333 through 334 and (name \ N or name CA or name C or name O or name CB )) or resid 335 through 340 or resi \ d 343 through 377 or (resid 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 385 or (resid 386 and (name N or name CA or name C \ or name O or name CB )) or resid 387 through 388 or (resid 389 and (name N or n \ ame CA or name C or name O or name CB )) or resid 390 through 443 or (resid 444 \ and (name N or name CA or name C or name O or name CB )) or resid 445 through 44 \ 8 or (resid 449 and (name N or name CA or name C or name O or name CB )) or resi \ d 450 through 573 or (resid 574 through 575 and (name N or name CA or name C or \ name O or name CB )) or resid 576 through 621 or resid 639 through 744 or (resid \ 745 and (name N or name CA or name C or name O or name CB )) or resid 746 throu \ gh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 through 785 or (resid 786 and (name N or name CA or name C or name O \ or name CB )) or resid 787 through 813 or (resid 814 and (name N or name CA or n \ ame C or name O or name CB )) or resid 815 through 826 or resid 855 through 949 \ or (resid 950 and (name N or name CA or name C or name O or name CB )) or resid \ 951 through 984 or (resid 985 and (name N or name CA or name C or name O or name \ CB )) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA \ or name C or name O or name CB )) or resid 990 through 993 or (resid 994 and (n \ ame N or name CA or name C or name O or name CB )) or resid 995 through 1117 or \ (resid 1118 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 19 through 1138 or resid 1301 through 1305)) selection = (chain 'B' and (resid 28 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or (resid 80 through 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 95 or (resid 96 through 97 and (n \ ame N or name CA or name C or name O or name CB )) or resid 98 or (resid 99 and \ (name N or name CA or name C or name O or name CB )) or resid 100 through 101 or \ (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 3 through 108 or (resid 109 through 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 or (resid 113 and (name N or name CA or name C or \ name O or name CB )) or resid 114 or (resid 115 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 121 or (resid 122 through 125 and \ (name N or name CA or name C or name O or name CB )) or resid 126 through 128 or \ (resid 129 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 0 through 131 or (resid 132 through 138 and (name N or name CA or name C or name \ O or name CB )) or resid 139 or (resid 140 through 141 and (name N or name CA o \ r name C or name O or name CB )) or resid 155 or (resid 156 and (name N or name \ CA or name C or name O or name CB )) or resid 157 or (resid 158 and (name N or n \ ame CA or name C or name O or name CB )) or resid 159 through 168 or (resid 169 \ through 170 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 1 through 173 or (resid 187 and (name N or name CA or name C or name O or name C \ B )) or resid 188 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 196 or (resid 197 through 198 and (nam \ e N or name CA or name C or name O or name CB )) or resid 199 through 205 or (re \ sid 206 through 207 and (name N or name CA or name C or name O or name CB )) or \ resid 208 through 209 or (resid 210 and (name N or name CA or name C or name O o \ r name CB )) or resid 211 through 213 or (resid 214 and (name N or name CA or na \ me C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 243 or resid 2 \ 63 through 332 or (resid 333 through 334 and (name N or name CA or name C or nam \ e O or name CB )) or resid 335 through 340 or resid 343 through 385 or (resid 38 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 387 through \ 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or re \ sid 390 through 443 or (resid 444 and (name N or name CA or name C or name O or \ name CB )) or resid 445 through 448 or (resid 449 and (name N or name CA or name \ C or name O or name CB )) or resid 450 through 537 or (resid 538 and (name N or \ name CA or name C or name O or name CB )) or resid 539 through 573 or (resid 57 \ 4 through 575 and (name N or name CA or name C or name O or name CB )) or resid \ 576 through 582 or (resid 583 and (name N or name CA or name C or name O or name \ CB )) or resid 584 through 589 or (resid 590 and (name N or name CA or name C o \ r name O or name CB )) or resid 591 through 621 or resid 639 through 744 or (res \ id 745 and (name N or name CA or name C or name O or name CB )) or resid 746 thr \ ough 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) \ or resid 749 through 785 or (resid 786 and (name N or name CA or name C or name \ O or name CB )) or resid 787 through 795 or (resid 796 and (name N or name CA or \ name C or name O or name CB )) or resid 797 through 813 or (resid 814 and (name \ N or name CA or name C or name O or name CB )) or resid 815 through 826 or resi \ d 855 through 949 or (resid 950 and (name N or name CA or name C or name O or na \ me CB )) or resid 951 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and \ (name N or name CA or name C or name O or name CB )) or resid 990 through 993 or \ (resid 994 and (name N or name CA or name C or name O or name CB )) or resid 99 \ 5 through 1044 or (resid 1045 and (name N or name CA or name C or name O or name \ CB )) or resid 1046 through 1117 or (resid 1118 and (name N or name CA or name \ C or name O or name CB )) or resid 1119 through 1138 or resid 1301 through 1305) \ ) selection = (chain 'C' and (resid 28 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 or (resid 99 and ( \ name N or name CA or name C or name O or name CB )) or resid 100 through 121 or \ (resid 122 through 125 and (name N or name CA or name C or name O or name CB )) \ or resid 126 through 133 or (resid 134 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 through 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 155 or (resid 156 and (name \ N or name CA or name C or name O or name CB )) or resid 157 through 168 or (res \ id 169 through 170 and (name N or name CA or name C or name O or name CB )) or r \ esid 171 through 189 or (resid 190 and (name N or name CA or name C or name O or \ name CB )) or resid 191 through 209 or (resid 210 and (name N or name CA or nam \ e C or name O or name CB )) or resid 211 through 217 or (resid 218 and (name N o \ r name CA or name C or name O or name CB )) or resid 219 through 236 or (resid 2 \ 37 and (name N or name CA or name C or name O or name CB )) or resid 238 through \ 242 or resid 262 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB )) or resid 379 through 442 or (resid 443 through 444 and (nam \ e N or name CA or name C or name O or name CB )) or resid 445 through 537 or (re \ sid 538 and (name N or name CA or name C or name O or name CB )) or resid 539 th \ rough 582 or (resid 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 589 or (resid 590 and (name N or name CA or name C or name \ O or name CB )) or resid 591 through 826 or resid 855 through 1044 or (resid 10 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 1046 throug \ h 1138 or resid 1301 through 1305)) } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } 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: 11.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 57.040 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25033 Z= 0.163 Angle : 0.596 11.822 34185 Z= 0.306 Chirality : 0.046 0.524 3994 Planarity : 0.004 0.050 4378 Dihedral : 19.037 124.030 9302 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 0.30 % Allowed : 30.57 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.14), residues: 3065 helix: -0.91 (0.21), residues: 598 sheet: -0.23 (0.21), residues: 610 loop : -1.98 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.001 PHE C 347 TYR 0.013 0.001 TYR A 279 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 26) link_NAG-ASN : angle 2.49481 ( 78) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 1.35942 ( 18) hydrogen bonds : bond 0.28753 ( 748) hydrogen bonds : angle 8.66234 ( 2067) SS BOND : bond 0.00455 ( 33) SS BOND : angle 1.69789 ( 66) covalent geometry : bond 0.00355 (24968) covalent geometry : angle 0.57981 (34023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 365 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.7403 (t0) cc_final: 0.6873 (p0) REVERT: A 226 LEU cc_start: 0.7848 (mt) cc_final: 0.7631 (mt) REVERT: A 558 LYS cc_start: 0.7724 (tptp) cc_final: 0.7312 (mttm) REVERT: A 1014 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7942 (mtt180) REVERT: B 49 HIS cc_start: 0.8092 (t70) cc_final: 0.7850 (t-170) REVERT: B 55 PHE cc_start: 0.6995 (m-80) cc_final: 0.6601 (m-80) REVERT: B 153 MET cc_start: 0.2616 (mtt) cc_final: 0.1102 (mpp) REVERT: B 169 GLU cc_start: 0.7511 (tp30) cc_final: 0.7228 (mp0) REVERT: B 1001 LEU cc_start: 0.8813 (tp) cc_final: 0.8605 (tp) REVERT: C 740 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7420 (tpp) REVERT: C 823 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6622 (t80) REVERT: C 1041 ASP cc_start: 0.7727 (m-30) cc_final: 0.7509 (t0) outliers start: 8 outliers final: 0 residues processed: 369 average time/residue: 0.3686 time to fit residues: 211.6640 Evaluate side-chains 218 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 823 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 chunk 181 optimal weight: 0.9980 chunk 282 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 784 GLN B 804 GLN B 901 GLN B 935 GLN B 949 GLN B1005 GLN C 218 GLN C 658 ASN C 762 GLN C 957 GLN C1002 GLN C1106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.192746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131872 restraints weight = 32852.473| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.32 r_work: 0.3160 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25033 Z= 0.135 Angle : 0.619 11.724 34185 Z= 0.318 Chirality : 0.047 0.469 3994 Planarity : 0.005 0.048 4378 Dihedral : 11.644 110.046 4004 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 4.15 % Allowed : 25.62 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3065 helix: -0.03 (0.22), residues: 605 sheet: 0.04 (0.23), residues: 551 loop : -1.94 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS B1083 PHE 0.026 0.001 PHE B 140 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 26) link_NAG-ASN : angle 2.69985 ( 78) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 1.84793 ( 18) hydrogen bonds : bond 0.06951 ( 748) hydrogen bonds : angle 6.11665 ( 2067) SS BOND : bond 0.00490 ( 33) SS BOND : angle 1.56714 ( 66) covalent geometry : bond 0.00290 (24968) covalent geometry : angle 0.60169 (34023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 229 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.7849 (t0) cc_final: 0.6929 (p0) REVERT: A 191 GLU cc_start: 0.8251 (mp0) cc_final: 0.7986 (mp0) REVERT: A 195 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8003 (ptmm) REVERT: A 207 HIS cc_start: 0.8010 (t-90) cc_final: 0.7793 (t70) REVERT: A 321 GLN cc_start: 0.8246 (mm110) cc_final: 0.8027 (mm110) REVERT: A 558 LYS cc_start: 0.8061 (tptp) cc_final: 0.7192 (mttm) REVERT: A 984 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 1014 ARG cc_start: 0.8813 (ttm170) cc_final: 0.8543 (mtt90) REVERT: A 1038 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8731 (mmtp) REVERT: B 49 HIS cc_start: 0.8580 (t70) cc_final: 0.8231 (t70) REVERT: B 55 PHE cc_start: 0.7186 (m-80) cc_final: 0.6606 (m-80) REVERT: B 115 GLN cc_start: 0.3806 (OUTLIER) cc_final: 0.3184 (tm-30) REVERT: B 153 MET cc_start: 0.2632 (mtt) cc_final: 0.1029 (mpp) REVERT: B 169 GLU cc_start: 0.7711 (tp30) cc_final: 0.7435 (mp0) REVERT: B 170 TYR cc_start: 0.8659 (t80) cc_final: 0.8191 (t80) REVERT: B 202 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6727 (mtpt) REVERT: B 355 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7720 (ttp-170) REVERT: B 583 GLU cc_start: 0.6794 (tp30) cc_final: 0.6590 (tp30) REVERT: C 192 PHE cc_start: 0.8627 (m-80) cc_final: 0.8363 (m-80) REVERT: C 568 ASP cc_start: 0.8279 (t70) cc_final: 0.8021 (p0) REVERT: C 615 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8801 (m) REVERT: C 740 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8716 (tpt) REVERT: C 811 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7130 (mttt) REVERT: C 970 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: C 1041 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8195 (t0) outliers start: 109 outliers final: 48 residues processed: 323 average time/residue: 0.3231 time to fit residues: 169.6081 Evaluate side-chains 255 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 305 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 282 optimal weight: 0.0980 chunk 39 optimal weight: 0.0270 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 279 optimal weight: 0.0020 chunk 121 optimal weight: 0.0010 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN C 658 ASN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.194666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134764 restraints weight = 32873.441| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.41 r_work: 0.3196 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25033 Z= 0.109 Angle : 0.568 11.751 34185 Z= 0.285 Chirality : 0.045 0.487 3994 Planarity : 0.004 0.056 4378 Dihedral : 9.732 104.920 4002 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 2.89 % Allowed : 26.23 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3065 helix: 0.50 (0.22), residues: 591 sheet: 0.10 (0.22), residues: 553 loop : -1.88 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.000 HIS B1083 PHE 0.013 0.001 PHE B 855 TYR 0.017 0.001 TYR B1067 ARG 0.014 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 26) link_NAG-ASN : angle 2.52227 ( 78) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 2.09012 ( 18) hydrogen bonds : bond 0.05157 ( 748) hydrogen bonds : angle 5.49123 ( 2067) SS BOND : bond 0.00374 ( 33) SS BOND : angle 1.17237 ( 66) covalent geometry : bond 0.00222 (24968) covalent geometry : angle 0.55196 (34023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.5535 (mp) REVERT: A 164 ASN cc_start: 0.7875 (m-40) cc_final: 0.6948 (p0) REVERT: A 226 LEU cc_start: 0.8374 (mt) cc_final: 0.8130 (mt) REVERT: A 558 LYS cc_start: 0.8032 (tptp) cc_final: 0.7114 (mttm) REVERT: A 663 ASP cc_start: 0.7834 (p0) cc_final: 0.7438 (p0) REVERT: A 984 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7739 (mt) REVERT: A 1014 ARG cc_start: 0.8811 (ttm170) cc_final: 0.8552 (mtt90) REVERT: A 1038 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8697 (mmtp) REVERT: B 49 HIS cc_start: 0.8589 (t70) cc_final: 0.8282 (t70) REVERT: B 55 PHE cc_start: 0.7042 (m-80) cc_final: 0.6602 (m-80) REVERT: B 115 GLN cc_start: 0.3933 (OUTLIER) cc_final: 0.3381 (tm-30) REVERT: B 153 MET cc_start: 0.2604 (mtt) cc_final: 0.0981 (mpp) REVERT: B 170 TYR cc_start: 0.8561 (t80) cc_final: 0.8237 (t80) REVERT: B 396 TYR cc_start: 0.7205 (m-80) cc_final: 0.6502 (m-10) REVERT: C 615 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8779 (m) REVERT: C 740 MET cc_start: 0.8931 (mmm) cc_final: 0.8639 (tpt) REVERT: C 811 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7069 (mttt) REVERT: C 970 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 1041 ASP cc_start: 0.8583 (m-30) cc_final: 0.8179 (t0) outliers start: 76 outliers final: 46 residues processed: 272 average time/residue: 0.3321 time to fit residues: 147.3447 Evaluate side-chains 240 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 82 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 949 GLN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.193910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132658 restraints weight = 33245.208| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.49 r_work: 0.3133 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25033 Z= 0.130 Angle : 0.581 11.963 34185 Z= 0.289 Chirality : 0.046 0.505 3994 Planarity : 0.004 0.050 4378 Dihedral : 8.961 101.260 3999 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 3.69 % Allowed : 25.69 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 3065 helix: 0.57 (0.22), residues: 591 sheet: 0.12 (0.22), residues: 561 loop : -1.89 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS B1083 PHE 0.013 0.001 PHE B 562 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 26) link_NAG-ASN : angle 2.64178 ( 78) link_BETA1-4 : bond 0.00560 ( 6) link_BETA1-4 : angle 1.96805 ( 18) hydrogen bonds : bond 0.05618 ( 748) hydrogen bonds : angle 5.31355 ( 2067) SS BOND : bond 0.00364 ( 33) SS BOND : angle 1.30723 ( 66) covalent geometry : bond 0.00307 (24968) covalent geometry : angle 0.56339 (34023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 185 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.5524 (mp) REVERT: A 164 ASN cc_start: 0.7913 (m-40) cc_final: 0.6948 (p0) REVERT: A 168 PHE cc_start: 0.7017 (m-10) cc_final: 0.6775 (m-10) REVERT: A 170 TYR cc_start: 0.7280 (t80) cc_final: 0.7018 (t80) REVERT: A 547 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8067 (t) REVERT: A 558 LYS cc_start: 0.8022 (tptp) cc_final: 0.7060 (mttm) REVERT: A 754 LEU cc_start: 0.9277 (mt) cc_final: 0.9063 (mm) REVERT: A 1014 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8506 (mtt90) REVERT: A 1038 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8689 (mmtp) REVERT: B 49 HIS cc_start: 0.8612 (t70) cc_final: 0.8250 (t70) REVERT: B 115 GLN cc_start: 0.3847 (OUTLIER) cc_final: 0.3111 (tm-30) REVERT: B 116 SER cc_start: 0.6422 (m) cc_final: 0.5781 (p) REVERT: B 153 MET cc_start: 0.2622 (mtt) cc_final: 0.1071 (mpp) REVERT: B 170 TYR cc_start: 0.8560 (t80) cc_final: 0.8304 (t80) REVERT: B 353 TRP cc_start: 0.8233 (p-90) cc_final: 0.7994 (p-90) REVERT: B 396 TYR cc_start: 0.7228 (m-80) cc_final: 0.6519 (m-10) REVERT: B 658 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7774 (p0) REVERT: C 811 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7023 (mttt) REVERT: C 970 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: C 1041 ASP cc_start: 0.8652 (m-30) cc_final: 0.8327 (t0) outliers start: 97 outliers final: 70 residues processed: 262 average time/residue: 0.3209 time to fit residues: 138.3966 Evaluate side-chains 253 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 65 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 218 GLN C 901 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125711 restraints weight = 33189.108| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.31 r_work: 0.3062 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 25033 Z= 0.303 Angle : 0.754 14.164 34185 Z= 0.383 Chirality : 0.053 0.574 3994 Planarity : 0.006 0.057 4378 Dihedral : 8.968 96.988 3999 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 5.56 % Allowed : 24.17 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3065 helix: -0.06 (0.21), residues: 590 sheet: -0.11 (0.22), residues: 588 loop : -2.11 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C1102 HIS 0.007 0.002 HIS A1058 PHE 0.029 0.002 PHE D 68 TYR 0.024 0.002 TYR B1067 ARG 0.010 0.001 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 26) link_NAG-ASN : angle 3.31495 ( 78) link_BETA1-4 : bond 0.00580 ( 6) link_BETA1-4 : angle 1.88951 ( 18) hydrogen bonds : bond 0.08780 ( 748) hydrogen bonds : angle 5.61825 ( 2067) SS BOND : bond 0.00705 ( 33) SS BOND : angle 2.10857 ( 66) covalent geometry : bond 0.00773 (24968) covalent geometry : angle 0.73167 (34023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 177 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 ASP cc_start: 0.3148 (OUTLIER) cc_final: 0.2531 (t70) REVERT: A 52 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 100 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 164 ASN cc_start: 0.7739 (t0) cc_final: 0.6570 (p0) REVERT: A 265 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.4315 (t80) REVERT: A 558 LYS cc_start: 0.7990 (tptp) cc_final: 0.6925 (mttm) REVERT: A 855 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5943 (m-80) REVERT: A 984 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7834 (mt) REVERT: B 49 HIS cc_start: 0.8655 (t70) cc_final: 0.8343 (t70) REVERT: B 153 MET cc_start: 0.2664 (mtt) cc_final: 0.1098 (mpp) REVERT: B 170 TYR cc_start: 0.8535 (t80) cc_final: 0.8090 (t80) REVERT: B 202 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6840 (mtpt) REVERT: B 396 TYR cc_start: 0.7218 (m-80) cc_final: 0.6994 (m-80) REVERT: B 658 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 990 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: C 646 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7347 (tpt90) REVERT: C 895 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: C 970 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8000 (m-80) outliers start: 146 outliers final: 95 residues processed: 303 average time/residue: 0.2939 time to fit residues: 149.1113 Evaluate side-chains 276 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 171 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 149 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 118 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 242 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN C 935 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.191006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127532 restraints weight = 32907.627| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.28 r_work: 0.3113 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25033 Z= 0.125 Angle : 0.597 12.299 34185 Z= 0.298 Chirality : 0.046 0.530 3994 Planarity : 0.004 0.051 4378 Dihedral : 8.248 92.551 3999 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 3.54 % Allowed : 26.23 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3065 helix: 0.34 (0.22), residues: 597 sheet: -0.02 (0.21), residues: 597 loop : -1.99 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 PHE 0.020 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 26) link_NAG-ASN : angle 2.77628 ( 78) link_BETA1-4 : bond 0.00652 ( 6) link_BETA1-4 : angle 2.12194 ( 18) hydrogen bonds : bond 0.05702 ( 748) hydrogen bonds : angle 5.20414 ( 2067) SS BOND : bond 0.00399 ( 33) SS BOND : angle 1.37281 ( 66) covalent geometry : bond 0.00284 (24968) covalent geometry : angle 0.57789 (34023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 173 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.0973 (mmp) cc_final: 0.0547 (mmt) REVERT: A 52 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 100 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 164 ASN cc_start: 0.7705 (t0) cc_final: 0.6616 (p0) REVERT: A 558 LYS cc_start: 0.7926 (tptp) cc_final: 0.6859 (mmtt) REVERT: B 49 HIS cc_start: 0.8642 (t70) cc_final: 0.8328 (t70) REVERT: B 115 GLN cc_start: 0.3621 (OUTLIER) cc_final: 0.2806 (tm-30) REVERT: B 116 SER cc_start: 0.6316 (m) cc_final: 0.5712 (p) REVERT: B 190 ARG cc_start: 0.7461 (mtt-85) cc_final: 0.7093 (tpp80) REVERT: B 202 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6776 (mtpt) REVERT: B 396 TYR cc_start: 0.7205 (m-80) cc_final: 0.6918 (m-80) REVERT: B 658 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7755 (p0) REVERT: C 646 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7253 (tpt90) REVERT: C 970 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7851 (m-80) outliers start: 93 outliers final: 66 residues processed: 253 average time/residue: 0.3184 time to fit residues: 133.7069 Evaluate side-chains 240 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 264 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129301 restraints weight = 33079.892| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.43 r_work: 0.3085 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25033 Z= 0.149 Angle : 0.612 12.711 34185 Z= 0.305 Chirality : 0.047 0.532 3994 Planarity : 0.004 0.053 4378 Dihedral : 7.977 88.642 3999 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 4.04 % Allowed : 26.00 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3065 helix: 0.35 (0.22), residues: 604 sheet: 0.02 (0.21), residues: 600 loop : -2.00 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.001 PHE C 192 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 26) link_NAG-ASN : angle 2.83216 ( 78) link_BETA1-4 : bond 0.00669 ( 6) link_BETA1-4 : angle 2.11456 ( 18) hydrogen bonds : bond 0.06135 ( 748) hydrogen bonds : angle 5.13281 ( 2067) SS BOND : bond 0.00408 ( 33) SS BOND : angle 1.41325 ( 66) covalent geometry : bond 0.00361 (24968) covalent geometry : angle 0.59300 (34023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 164 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.0756 (mmp) cc_final: 0.0318 (mmt) REVERT: A 52 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 100 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 164 ASN cc_start: 0.7707 (t0) cc_final: 0.6595 (p0) REVERT: A 265 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.4189 (t80) REVERT: A 277 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9043 (mt) REVERT: A 558 LYS cc_start: 0.7968 (tptp) cc_final: 0.6852 (mmtt) REVERT: B 49 HIS cc_start: 0.8662 (t70) cc_final: 0.8360 (t70) REVERT: B 153 MET cc_start: 0.2996 (mtt) cc_final: 0.1427 (mpp) REVERT: B 190 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.7071 (tpp80) REVERT: B 202 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6849 (mtpt) REVERT: B 396 TYR cc_start: 0.7283 (m-80) cc_final: 0.6994 (m-80) REVERT: B 658 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7767 (p0) REVERT: B 990 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: C 190 ARG cc_start: 0.7365 (tpt170) cc_final: 0.6894 (tpp-160) REVERT: C 291 CYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7385 (t) REVERT: C 646 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7352 (tpt90) REVERT: C 895 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8795 (pt0) REVERT: C 970 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7952 (m-80) outliers start: 106 outliers final: 81 residues processed: 254 average time/residue: 0.3078 time to fit residues: 129.4260 Evaluate side-chains 255 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 165 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 267 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 208 optimal weight: 0.2980 chunk 305 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128373 restraints weight = 33132.438| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.39 r_work: 0.3081 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25033 Z= 0.149 Angle : 0.611 12.777 34185 Z= 0.304 Chirality : 0.047 0.534 3994 Planarity : 0.004 0.054 4378 Dihedral : 7.630 87.723 3999 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 4.07 % Allowed : 25.96 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3065 helix: 0.39 (0.22), residues: 601 sheet: -0.00 (0.21), residues: 605 loop : -2.03 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.022 0.001 PHE B 643 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 26) link_NAG-ASN : angle 2.87251 ( 78) link_BETA1-4 : bond 0.00750 ( 6) link_BETA1-4 : angle 2.30808 ( 18) hydrogen bonds : bond 0.06060 ( 748) hydrogen bonds : angle 5.07970 ( 2067) SS BOND : bond 0.00390 ( 33) SS BOND : angle 1.42828 ( 66) covalent geometry : bond 0.00362 (24968) covalent geometry : angle 0.59069 (34023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 167 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.0908 (mmp) cc_final: 0.0490 (mmt) REVERT: A 52 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 164 ASN cc_start: 0.7631 (t0) cc_final: 0.6442 (p0) REVERT: A 168 PHE cc_start: 0.7226 (m-10) cc_final: 0.6995 (m-10) REVERT: A 265 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.4161 (t80) REVERT: A 277 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9060 (mt) REVERT: A 558 LYS cc_start: 0.7860 (tptp) cc_final: 0.6765 (mmtt) REVERT: B 49 HIS cc_start: 0.8675 (t70) cc_final: 0.8371 (t70) REVERT: B 115 GLN cc_start: 0.3583 (OUTLIER) cc_final: 0.2932 (tm-30) REVERT: B 153 MET cc_start: 0.3008 (mtt) cc_final: 0.1424 (mpp) REVERT: B 191 GLU cc_start: 0.8106 (pm20) cc_final: 0.7845 (mt-10) REVERT: B 202 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6786 (mtpt) REVERT: B 396 TYR cc_start: 0.7310 (m-80) cc_final: 0.7011 (m-80) REVERT: B 658 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7801 (p0) REVERT: B 868 GLU cc_start: 0.8429 (mp0) cc_final: 0.7995 (mm-30) REVERT: B 990 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: C 291 CYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7399 (t) REVERT: C 646 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7434 (tpt90) REVERT: C 970 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7950 (m-80) outliers start: 107 outliers final: 90 residues processed: 257 average time/residue: 0.3108 time to fit residues: 132.7137 Evaluate side-chains 261 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 163 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 210 optimal weight: 0.0970 chunk 164 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN B 321 GLN B 613 GLN B1058 HIS C 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.188521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124654 restraints weight = 33242.353| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.23 r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25033 Z= 0.151 Angle : 0.612 12.933 34185 Z= 0.304 Chirality : 0.047 0.536 3994 Planarity : 0.004 0.054 4378 Dihedral : 7.349 86.736 3999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 4.23 % Allowed : 25.69 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3065 helix: 0.39 (0.22), residues: 601 sheet: 0.04 (0.21), residues: 605 loop : -2.02 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.001 PHE C 192 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 26) link_NAG-ASN : angle 2.99846 ( 78) link_BETA1-4 : bond 0.00754 ( 6) link_BETA1-4 : angle 2.43879 ( 18) hydrogen bonds : bond 0.06093 ( 748) hydrogen bonds : angle 5.03835 ( 2067) SS BOND : bond 0.00384 ( 33) SS BOND : angle 1.45649 ( 66) covalent geometry : bond 0.00369 (24968) covalent geometry : angle 0.59000 (34023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 162 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.0789 (mmp) cc_final: 0.0261 (mmt) REVERT: A 52 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 164 ASN cc_start: 0.7686 (t0) cc_final: 0.6466 (p0) REVERT: A 265 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.4157 (t80) REVERT: A 277 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9029 (mt) REVERT: A 558 LYS cc_start: 0.7809 (tptp) cc_final: 0.6696 (mmtt) REVERT: B 49 HIS cc_start: 0.8654 (t70) cc_final: 0.8338 (t70) REVERT: B 115 GLN cc_start: 0.3600 (OUTLIER) cc_final: 0.2792 (tm-30) REVERT: B 116 SER cc_start: 0.6431 (m) cc_final: 0.5790 (p) REVERT: B 153 MET cc_start: 0.2920 (mtt) cc_final: 0.1367 (mpp) REVERT: B 191 GLU cc_start: 0.8057 (pm20) cc_final: 0.7809 (mt-10) REVERT: B 202 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6697 (mtpt) REVERT: B 658 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7784 (p0) REVERT: B 990 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 190 ARG cc_start: 0.7373 (tpt170) cc_final: 0.6888 (tpp-160) REVERT: C 291 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7317 (t) REVERT: C 646 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7419 (tpt90) REVERT: C 895 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8821 (pt0) REVERT: C 970 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 1041 ASP cc_start: 0.8639 (m-30) cc_final: 0.8249 (t0) outliers start: 111 outliers final: 95 residues processed: 258 average time/residue: 0.3183 time to fit residues: 135.7217 Evaluate side-chains 264 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 160 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 24 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 182 optimal weight: 0.0000 chunk 73 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.189234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129506 restraints weight = 33187.618| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.33 r_work: 0.3135 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25033 Z= 0.115 Angle : 0.588 12.481 34185 Z= 0.291 Chirality : 0.045 0.524 3994 Planarity : 0.004 0.052 4378 Dihedral : 7.107 86.353 3999 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 3.77 % Allowed : 26.23 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3065 helix: 0.57 (0.22), residues: 602 sheet: 0.03 (0.21), residues: 617 loop : -1.98 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 PHE 0.021 0.001 PHE C 192 TYR 0.037 0.001 TYR A 170 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 26) link_NAG-ASN : angle 2.99364 ( 78) link_BETA1-4 : bond 0.00825 ( 6) link_BETA1-4 : angle 2.54739 ( 18) hydrogen bonds : bond 0.05316 ( 748) hydrogen bonds : angle 4.94160 ( 2067) SS BOND : bond 0.00341 ( 33) SS BOND : angle 1.22903 ( 66) covalent geometry : bond 0.00260 (24968) covalent geometry : angle 0.56562 (34023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 158 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.0752 (mmp) cc_final: 0.0289 (mmt) REVERT: A 52 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 164 ASN cc_start: 0.7664 (t0) cc_final: 0.6482 (p0) REVERT: A 195 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8275 (mtmt) REVERT: A 226 LEU cc_start: 0.8412 (mt) cc_final: 0.8145 (mt) REVERT: A 558 LYS cc_start: 0.7774 (tptp) cc_final: 0.6687 (mmtt) REVERT: B 49 HIS cc_start: 0.8628 (t70) cc_final: 0.8329 (t70) REVERT: B 115 GLN cc_start: 0.3723 (OUTLIER) cc_final: 0.2887 (tm-30) REVERT: B 116 SER cc_start: 0.6479 (m) cc_final: 0.5818 (p) REVERT: B 153 MET cc_start: 0.2975 (mtt) cc_final: 0.1391 (mpp) REVERT: B 191 GLU cc_start: 0.8009 (pm20) cc_final: 0.7781 (mt-10) REVERT: B 202 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6705 (mtpt) REVERT: B 396 TYR cc_start: 0.7265 (m-80) cc_final: 0.6950 (m-80) REVERT: B 658 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7782 (p0) REVERT: B 985 ASP cc_start: 0.7034 (p0) cc_final: 0.6556 (m-30) REVERT: B 990 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: C 190 ARG cc_start: 0.7338 (tpt170) cc_final: 0.6839 (tpp-160) REVERT: C 291 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7184 (t) REVERT: C 646 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7495 (tpt90) REVERT: C 895 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8806 (pt0) REVERT: C 970 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: C 1041 ASP cc_start: 0.8632 (m-30) cc_final: 0.8288 (t0) outliers start: 99 outliers final: 81 residues processed: 244 average time/residue: 0.3091 time to fit residues: 125.2116 Evaluate side-chains 245 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 156 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 299 optimal weight: 2.9990 chunk 300 optimal weight: 0.1980 chunk 207 optimal weight: 0.0980 chunk 202 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B1058 HIS C 901 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.190282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129760 restraints weight = 33201.833| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.22 r_work: 0.3150 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25033 Z= 0.103 Angle : 0.571 12.154 34185 Z= 0.283 Chirality : 0.045 0.511 3994 Planarity : 0.004 0.049 4378 Dihedral : 6.845 85.508 3999 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.20 % Allowed : 26.80 % Favored : 70.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3065 helix: 0.77 (0.22), residues: 602 sheet: 0.12 (0.21), residues: 600 loop : -1.91 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.003 0.001 HIS B1083 PHE 0.021 0.001 PHE C 192 TYR 0.021 0.001 TYR B 170 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 26) link_NAG-ASN : angle 2.96984 ( 78) link_BETA1-4 : bond 0.00837 ( 6) link_BETA1-4 : angle 2.59434 ( 18) hydrogen bonds : bond 0.04743 ( 748) hydrogen bonds : angle 4.80561 ( 2067) SS BOND : bond 0.00301 ( 33) SS BOND : angle 1.10417 ( 66) covalent geometry : bond 0.00222 (24968) covalent geometry : angle 0.54881 (34023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16162.47 seconds wall clock time: 279 minutes 54.20 seconds (16794.20 seconds total)