Starting phenix.real_space_refine on Thu Mar 5 10:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.map" model { file = "/net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mtc_23982/03_2026/7mtc_23982.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 91 5.16 5 C 13511 2.51 5 N 3448 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21178 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7139 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 45, 'TRANS': 868} Chain breaks: 15 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6435 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 43, 'TRANS': 786} Chain breaks: 13 Chain: "C" Number of atoms: 7016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7016 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 46, 'TRANS': 851} Chain breaks: 16 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "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: "L" 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: "M" 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: "N" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.69, per 1000 atoms: 0.22 Number of scatterers: 21178 At special positions: 0 Unit cell: (131.67, 132.525, 164.16, 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 91 16.00 O 4128 8.00 N 3448 7.00 C 13511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 878.3 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4966 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 41 sheets defined 26.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.901A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.396A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.603A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.546A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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 758 through 783 removed outlier: 3.577A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.591A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.638A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 940 removed outlier: 4.180A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.102A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.667A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.783A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.834A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.959A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 984 removed outlier: 3.567A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.645A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.841A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.544A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 4.021A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.516A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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 761 through 783 removed outlier: 3.916A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.666A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.713A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.164A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.001A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.866A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.612A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 279 removed outlier: 6.707A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.196A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.820A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.424A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.819A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.440A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.570A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.071A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.887A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.664A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.463A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.721A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.988A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.569A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.584A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.545A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.669A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.801A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 842 hydrogen bonds defined for protein. 2337 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: 4.90 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4904 1.33 - 1.45: 5552 1.45 - 1.58: 11037 1.58 - 1.71: 0 1.71 - 1.83: 115 Bond restraints: 21608 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.19e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CA SER B 758 " pdb=" CB SER B 758 " ideal model delta sigma weight residual 1.531 1.426 0.105 3.12e-02 1.03e+03 1.12e+01 bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.68e+00 bond pdb=" CB VAL B1094 " pdb=" CG1 VAL B1094 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.17e+00 ... (remaining 21603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 28965 3.55 - 7.09: 369 7.09 - 10.64: 36 10.64 - 14.19: 5 14.19 - 17.73: 1 Bond angle restraints: 29376 Sorted by residual: angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 134.30 -12.76 1.91e+00 2.74e-01 4.46e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.72 106.41 7.31 1.30e+00 5.92e-01 3.16e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.25 -6.55 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.03 -6.33 1.22e+00 6.72e-01 2.69e+01 ... (remaining 29371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 12667 16.01 - 32.02: 541 32.02 - 48.03: 154 48.03 - 64.05: 46 64.05 - 80.06: 17 Dihedral angle restraints: 13425 sinusoidal: 5759 harmonic: 7666 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.73 63.73 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA ASN B 616 " pdb=" C ASN B 616 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 13422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3364 0.143 - 0.287: 161 0.287 - 0.430: 4 0.430 - 0.573: 0 0.573 - 0.717: 2 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3528 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 823 " -0.027 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE C 823 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 823 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 823 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 823 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 823 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 823 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 823 " -0.022 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A 823 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 823 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 823 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 823 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 823 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 823 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 800 " -0.026 2.00e-02 2.50e+03 2.69e-02 1.27e+01 pdb=" CG PHE A 800 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 800 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 800 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 800 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 800 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 800 " -0.007 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3284 2.76 - 3.29: 17642 3.29 - 3.83: 32646 3.83 - 4.36: 37650 4.36 - 4.90: 67458 Nonbonded interactions: 158680 Sorted by model distance: nonbonded pdb=" OE2 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.254 3.040 nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.338 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.354 3.040 ... (remaining 158675 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 27 through 65 or resid 81 through 95 or resid 100 through \ 121 or resid 126 through 131 or resid 169 through 241 or resid 265 through 343 o \ r resid 358 through 368 or resid 383 through 395 or resid 399 through 400 or res \ id 492 or resid 521 through 620 or resid 641 through 675 or resid 690 through 82 \ 6 or resid 855 through 940 or resid 943 through 1143 or resid 1301 through 1304) \ ) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 109 or resid 115 throug \ h 172 or resid 189 through 209 or resid 216 through 241 or resid 265 through 395 \ or resid 514 through 515 or resid 518 or resid 521 through 620 or resid 641 thr \ ough 675 or resid 690 through 940 or resid 943 through 1143 or resid 1302 throug \ h 1305)) selection = (chain 'C' and (resid 27 through 65 or resid 81 through 130 or resid 166 or resi \ d 169 through 172 or resid 189 through 241 or resid 265 through 343 or resid 358 \ through 368 or resid 383 through 395 or resid 399 through 400 or resid 492 or r \ esid 521 through 620 or resid 641 through 826 or resid 855 through 1143 or resid \ 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.310 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.013 0.121 21679 Z= 0.544 Angle : 1.159 17.735 29560 Z= 0.624 Chirality : 0.076 0.717 3531 Planarity : 0.009 0.077 3708 Dihedral : 10.878 80.057 8372 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.56 % Allowed : 2.33 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.14), residues: 2548 helix: -1.38 (0.17), residues: 628 sheet: -0.67 (0.21), residues: 566 loop : -2.76 (0.13), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A1019 TYR 0.043 0.005 TYR B 279 PHE 0.065 0.006 PHE C 823 TRP 0.049 0.006 TRP A 886 HIS 0.019 0.005 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01341 (21608) covalent geometry : angle 1.13514 (29376) SS BOND : bond 0.00657 ( 29) SS BOND : angle 3.10675 ( 58) hydrogen bonds : bond 0.20812 ( 806) hydrogen bonds : angle 7.36357 ( 2337) link_BETA1-4 : bond 0.00933 ( 14) link_BETA1-4 : angle 2.56440 ( 42) link_NAG-ASN : bond 0.00672 ( 28) link_NAG-ASN : angle 3.49728 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: B 809 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.7177 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8192 (mp0) cc_final: 0.7945 (mp0) REVERT: C 239 GLN cc_start: 0.8064 (pt0) cc_final: 0.7585 (pt0) outliers start: 13 outliers final: 3 residues processed: 292 average time/residue: 0.6642 time to fit residues: 219.3521 Evaluate side-chains 151 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 370 ASN A 414 GLN A 901 GLN A 957 GLN A1010 GLN B 207 HIS B 540 ASN B 606 ASN B 762 GLN B 804 GLN B 901 GLN B 935 GLN B 957 GLN B1002 GLN C 354 ASN C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.083133 restraints weight = 30124.001| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.26 r_work: 0.2850 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21679 Z= 0.143 Angle : 0.667 15.309 29560 Z= 0.337 Chirality : 0.047 0.301 3531 Planarity : 0.005 0.049 3708 Dihedral : 6.997 59.989 3670 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.90 % Allowed : 6.86 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 2548 helix: 0.43 (0.21), residues: 630 sheet: 0.10 (0.20), residues: 595 loop : -2.28 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 357 TYR 0.025 0.002 TYR B 904 PHE 0.019 0.002 PHE C 32 TRP 0.018 0.002 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00320 (21608) covalent geometry : angle 0.64751 (29376) SS BOND : bond 0.00281 ( 29) SS BOND : angle 1.36706 ( 58) hydrogen bonds : bond 0.06521 ( 806) hydrogen bonds : angle 5.58050 ( 2337) link_BETA1-4 : bond 0.00374 ( 14) link_BETA1-4 : angle 1.35216 ( 42) link_NAG-ASN : bond 0.00505 ( 28) link_NAG-ASN : angle 2.73823 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7161 (mmp-170) cc_final: 0.6917 (mmt90) REVERT: A 200 TYR cc_start: 0.7409 (m-80) cc_final: 0.6870 (m-80) REVERT: A 281 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: A 347 PHE cc_start: 0.5095 (OUTLIER) cc_final: 0.4295 (m-80) REVERT: A 529 LYS cc_start: 0.8366 (mppt) cc_final: 0.8022 (mmmt) REVERT: A 556 ASN cc_start: 0.7796 (t0) cc_final: 0.7563 (t0) REVERT: A 646 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8040 (mtm110) REVERT: A 654 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 740 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8195 (ttp) REVERT: A 1005 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8894 (mt0) REVERT: B 102 ARG cc_start: 0.7750 (mmm160) cc_final: 0.6916 (mmm-85) REVERT: B 271 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: B 314 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: B 809 PRO cc_start: 0.7595 (Cg_endo) cc_final: 0.7024 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6688 (p90) REVERT: B 988 GLU cc_start: 0.8631 (mp0) cc_final: 0.8112 (mp0) REVERT: C 33 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7479 (p) REVERT: C 239 GLN cc_start: 0.8068 (pt0) cc_final: 0.7584 (pt0) REVERT: C 560 LEU cc_start: 0.8125 (mt) cc_final: 0.7645 (mp) REVERT: C 1092 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7866 (pm20) outliers start: 44 outliers final: 8 residues processed: 214 average time/residue: 0.6597 time to fit residues: 160.8327 Evaluate side-chains 167 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 16 optimal weight: 0.2980 chunk 221 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 23 optimal weight: 4.9990 chunk 163 optimal weight: 0.0050 chunk 174 optimal weight: 10.0000 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B 957 GLN B1002 GLN C 87 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084809 restraints weight = 30131.845| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.26 r_work: 0.2881 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21679 Z= 0.111 Angle : 0.602 14.080 29560 Z= 0.299 Chirality : 0.045 0.254 3531 Planarity : 0.004 0.049 3708 Dihedral : 6.252 59.290 3669 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.90 % Allowed : 8.32 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2548 helix: 1.20 (0.22), residues: 629 sheet: 0.34 (0.21), residues: 592 loop : -1.93 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.019 0.001 TYR B 904 PHE 0.018 0.001 PHE A 32 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (21608) covalent geometry : angle 0.57875 (29376) SS BOND : bond 0.00403 ( 29) SS BOND : angle 1.32531 ( 58) hydrogen bonds : bond 0.05276 ( 806) hydrogen bonds : angle 5.14339 ( 2337) link_BETA1-4 : bond 0.00430 ( 14) link_BETA1-4 : angle 1.24118 ( 42) link_NAG-ASN : bond 0.00443 ( 28) link_NAG-ASN : angle 2.86673 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7444 (m-80) cc_final: 0.6853 (m-80) REVERT: A 281 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: A 347 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4483 (m-80) REVERT: A 428 ASP cc_start: 0.7832 (p0) cc_final: 0.7632 (p0) REVERT: A 529 LYS cc_start: 0.8362 (mppt) cc_final: 0.8047 (mmmt) REVERT: A 556 ASN cc_start: 0.7824 (t0) cc_final: 0.7537 (t0) REVERT: A 646 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8025 (ttp80) REVERT: A 654 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: A 740 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8225 (ttp) REVERT: A 780 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 790 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8595 (mtmt) REVERT: A 1005 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8824 (mt0) REVERT: B 102 ARG cc_start: 0.7748 (mmm160) cc_final: 0.7467 (mmm-85) REVERT: B 271 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: B 529 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7868 (mtpp) REVERT: B 581 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 809 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.6990 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8639 (mp0) cc_final: 0.8089 (mp0) REVERT: C 33 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 239 GLN cc_start: 0.8021 (pt0) cc_final: 0.7649 (pt0) REVERT: C 560 LEU cc_start: 0.8056 (mt) cc_final: 0.7559 (mp) REVERT: C 1092 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7816 (pm20) outliers start: 44 outliers final: 10 residues processed: 193 average time/residue: 0.5955 time to fit residues: 132.5106 Evaluate side-chains 165 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 231 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082588 restraints weight = 30113.309| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.28 r_work: 0.2842 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21679 Z= 0.133 Angle : 0.613 14.351 29560 Z= 0.305 Chirality : 0.046 0.256 3531 Planarity : 0.004 0.044 3708 Dihedral : 5.889 59.910 3669 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.54 % Allowed : 8.41 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2548 helix: 1.45 (0.22), residues: 636 sheet: 0.54 (0.21), residues: 600 loop : -1.77 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.022 0.001 TYR B1067 PHE 0.019 0.001 PHE C 32 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00307 (21608) covalent geometry : angle 0.59178 (29376) SS BOND : bond 0.00294 ( 29) SS BOND : angle 1.40425 ( 58) hydrogen bonds : bond 0.05947 ( 806) hydrogen bonds : angle 5.03192 ( 2337) link_BETA1-4 : bond 0.00412 ( 14) link_BETA1-4 : angle 1.20922 ( 42) link_NAG-ASN : bond 0.00430 ( 28) link_NAG-ASN : angle 2.79616 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6806 (mmt90) REVERT: A 200 TYR cc_start: 0.7479 (m-80) cc_final: 0.6827 (m-80) REVERT: A 281 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7171 (pp20) REVERT: A 304 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8258 (mttm) REVERT: A 347 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: A 529 LYS cc_start: 0.8383 (mppt) cc_final: 0.8107 (mmmt) REVERT: A 556 ASN cc_start: 0.7795 (t0) cc_final: 0.7488 (t0) REVERT: A 646 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: A 654 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 740 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8520 (ttt) REVERT: B 271 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: B 314 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: B 529 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7787 (mttm) REVERT: B 581 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 809 PRO cc_start: 0.7230 (Cg_endo) cc_final: 0.6775 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8663 (mp0) cc_final: 0.8102 (mp0) REVERT: C 33 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7462 (p) REVERT: C 239 GLN cc_start: 0.8013 (pt0) cc_final: 0.7718 (tt0) REVERT: C 560 LEU cc_start: 0.8067 (mt) cc_final: 0.7574 (mp) REVERT: C 855 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: C 1092 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7878 (pm20) outliers start: 59 outliers final: 15 residues processed: 201 average time/residue: 0.6095 time to fit residues: 140.4043 Evaluate side-chains 174 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 200 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B 935 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081488 restraints weight = 29781.764| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.23 r_work: 0.2822 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21679 Z= 0.161 Angle : 0.637 14.501 29560 Z= 0.320 Chirality : 0.047 0.262 3531 Planarity : 0.004 0.042 3708 Dihedral : 5.808 58.491 3669 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.63 % Allowed : 8.93 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2548 helix: 1.52 (0.22), residues: 630 sheet: 0.62 (0.21), residues: 606 loop : -1.72 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.025 0.002 TYR A 170 PHE 0.020 0.002 PHE C 32 TRP 0.008 0.001 TRP A 886 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00385 (21608) covalent geometry : angle 0.61580 (29376) SS BOND : bond 0.00317 ( 29) SS BOND : angle 1.44207 ( 58) hydrogen bonds : bond 0.06537 ( 806) hydrogen bonds : angle 5.05941 ( 2337) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 1.23943 ( 42) link_NAG-ASN : bond 0.00430 ( 28) link_NAG-ASN : angle 2.79518 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7294 (mmp-170) cc_final: 0.6785 (mmt90) REVERT: A 281 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: A 304 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8255 (mttm) REVERT: A 347 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.4624 (m-80) REVERT: A 462 LYS cc_start: 0.8809 (mppt) cc_final: 0.8559 (mppt) REVERT: A 529 LYS cc_start: 0.8398 (mppt) cc_final: 0.8096 (mmmt) REVERT: A 556 ASN cc_start: 0.7812 (t0) cc_final: 0.7481 (t0) REVERT: A 646 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8051 (ttp80) REVERT: A 654 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: A 740 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8542 (ttt) REVERT: B 271 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: B 314 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: B 529 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7745 (mttm) REVERT: B 581 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7618 (p) REVERT: B 809 PRO cc_start: 0.7242 (Cg_endo) cc_final: 0.6837 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8674 (mp0) cc_final: 0.8132 (mp0) REVERT: C 33 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7492 (p) REVERT: C 239 GLN cc_start: 0.8033 (pt0) cc_final: 0.7752 (tt0) REVERT: C 560 LEU cc_start: 0.8022 (mt) cc_final: 0.7525 (mp) REVERT: C 855 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: C 1092 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7846 (pm20) outliers start: 61 outliers final: 23 residues processed: 205 average time/residue: 0.5862 time to fit residues: 138.3890 Evaluate side-chains 180 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 224 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 121 ASN B 207 HIS B 804 GLN B 935 GLN B1002 GLN C 354 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080402 restraints weight = 29895.914| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.25 r_work: 0.2797 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21679 Z= 0.193 Angle : 0.673 15.358 29560 Z= 0.340 Chirality : 0.049 0.268 3531 Planarity : 0.005 0.041 3708 Dihedral : 5.836 58.312 3669 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.85 % Allowed : 8.93 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2548 helix: 1.42 (0.21), residues: 629 sheet: 0.65 (0.21), residues: 602 loop : -1.74 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.027 0.002 TYR B 904 PHE 0.021 0.002 PHE C 32 TRP 0.008 0.001 TRP A 886 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00471 (21608) covalent geometry : angle 0.65152 (29376) SS BOND : bond 0.00375 ( 29) SS BOND : angle 1.60411 ( 58) hydrogen bonds : bond 0.07197 ( 806) hydrogen bonds : angle 5.14531 ( 2337) link_BETA1-4 : bond 0.00346 ( 14) link_BETA1-4 : angle 1.31250 ( 42) link_NAG-ASN : bond 0.00435 ( 28) link_NAG-ASN : angle 2.89750 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 155 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6814 (mmt90) REVERT: A 281 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: A 304 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8294 (mttm) REVERT: A 347 PHE cc_start: 0.5176 (OUTLIER) cc_final: 0.4751 (m-80) REVERT: A 462 LYS cc_start: 0.8822 (mppt) cc_final: 0.8602 (mppt) REVERT: A 529 LYS cc_start: 0.8385 (mppt) cc_final: 0.8063 (mmmt) REVERT: A 556 ASN cc_start: 0.7804 (t0) cc_final: 0.7452 (t0) REVERT: A 646 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8087 (ttp80) REVERT: A 654 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: A 740 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8476 (ttt) REVERT: B 102 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: B 271 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: B 314 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8579 (tm-30) REVERT: B 528 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: B 529 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7746 (mttm) REVERT: B 581 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 809 PRO cc_start: 0.7184 (Cg_endo) cc_final: 0.6779 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6557 (p90) REVERT: B 988 GLU cc_start: 0.8684 (mp0) cc_final: 0.8405 (mp0) REVERT: C 239 GLN cc_start: 0.8060 (pt0) cc_final: 0.7753 (tt0) REVERT: C 560 LEU cc_start: 0.8006 (mt) cc_final: 0.7517 (mp) REVERT: C 855 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6950 (m-80) outliers start: 66 outliers final: 31 residues processed: 202 average time/residue: 0.5528 time to fit residues: 129.7398 Evaluate side-chains 191 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 173 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 203 optimal weight: 30.0000 chunk 60 optimal weight: 0.3980 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B1002 GLN C 354 ASN C 556 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080337 restraints weight = 29803.566| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.22 r_work: 0.2801 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21679 Z= 0.185 Angle : 0.672 15.884 29560 Z= 0.338 Chirality : 0.048 0.311 3531 Planarity : 0.004 0.041 3708 Dihedral : 5.735 58.066 3669 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.24 % Allowed : 10.18 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2548 helix: 1.45 (0.21), residues: 629 sheet: 0.65 (0.21), residues: 613 loop : -1.73 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.026 0.002 TYR A 170 PHE 0.018 0.002 PHE C 32 TRP 0.008 0.001 TRP A 886 HIS 0.007 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00451 (21608) covalent geometry : angle 0.65074 (29376) SS BOND : bond 0.00350 ( 29) SS BOND : angle 1.64488 ( 58) hydrogen bonds : bond 0.06998 ( 806) hydrogen bonds : angle 5.10875 ( 2337) link_BETA1-4 : bond 0.00363 ( 14) link_BETA1-4 : angle 1.30073 ( 42) link_NAG-ASN : bond 0.00423 ( 28) link_NAG-ASN : angle 2.86476 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6830 (mmt90) REVERT: A 200 TYR cc_start: 0.7419 (m-80) cc_final: 0.6496 (m-80) REVERT: A 281 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: A 304 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8301 (mttm) REVERT: A 462 LYS cc_start: 0.8825 (mppt) cc_final: 0.8559 (mppt) REVERT: A 529 LYS cc_start: 0.8420 (mppt) cc_final: 0.8085 (mmmt) REVERT: A 556 ASN cc_start: 0.7781 (t0) cc_final: 0.7421 (t0) REVERT: A 646 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8092 (ttp80) REVERT: A 654 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 740 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8503 (ttt) REVERT: B 102 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: B 271 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: B 314 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: B 528 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7748 (mtpt) REVERT: B 529 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7759 (mtpp) REVERT: B 581 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7603 (p) REVERT: B 809 PRO cc_start: 0.7269 (Cg_endo) cc_final: 0.6891 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6536 (p90) REVERT: B 988 GLU cc_start: 0.8683 (mp0) cc_final: 0.8389 (mp0) REVERT: C 560 LEU cc_start: 0.8007 (mt) cc_final: 0.7518 (mp) REVERT: C 794 ILE cc_start: 0.8042 (mm) cc_final: 0.7487 (pp) REVERT: C 855 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6943 (m-80) outliers start: 52 outliers final: 29 residues processed: 188 average time/residue: 0.5519 time to fit residues: 120.4648 Evaluate side-chains 182 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 260 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 233 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B1002 GLN C 354 ASN C 556 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083322 restraints weight = 29941.629| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.22 r_work: 0.2854 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21679 Z= 0.116 Angle : 0.599 14.869 29560 Z= 0.297 Chirality : 0.045 0.256 3531 Planarity : 0.004 0.039 3708 Dihedral : 5.281 56.425 3669 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.85 % Allowed : 10.87 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2548 helix: 1.74 (0.22), residues: 635 sheet: 0.83 (0.21), residues: 605 loop : -1.56 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.018 0.001 TYR A1067 PHE 0.019 0.001 PHE C 168 TRP 0.008 0.001 TRP B 886 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (21608) covalent geometry : angle 0.57904 (29376) SS BOND : bond 0.00273 ( 29) SS BOND : angle 1.22181 ( 58) hydrogen bonds : bond 0.05291 ( 806) hydrogen bonds : angle 4.83801 ( 2337) link_BETA1-4 : bond 0.00417 ( 14) link_BETA1-4 : angle 1.14701 ( 42) link_NAG-ASN : bond 0.00384 ( 28) link_NAG-ASN : angle 2.70817 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.6737 (mmt90) REVERT: A 200 TYR cc_start: 0.7439 (m-80) cc_final: 0.6494 (m-80) REVERT: A 281 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: A 304 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8287 (mttm) REVERT: A 347 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: A 462 LYS cc_start: 0.8837 (mppt) cc_final: 0.8489 (mppt) REVERT: A 529 LYS cc_start: 0.8394 (mppt) cc_final: 0.8055 (mmmt) REVERT: A 556 ASN cc_start: 0.7743 (t0) cc_final: 0.7377 (t0) REVERT: A 646 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: A 654 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 740 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8177 (ttp) REVERT: B 102 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7260 (mmm-85) REVERT: B 314 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: B 529 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7736 (mttm) REVERT: B 581 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7658 (p) REVERT: B 809 PRO cc_start: 0.7152 (Cg_endo) cc_final: 0.6796 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8680 (mp0) cc_final: 0.8137 (mp0) REVERT: C 556 ASN cc_start: 0.8278 (m-40) cc_final: 0.8030 (m-40) REVERT: C 560 LEU cc_start: 0.7969 (mt) cc_final: 0.7484 (mp) REVERT: C 794 ILE cc_start: 0.7924 (mm) cc_final: 0.7384 (pp) REVERT: C 855 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6882 (m-80) outliers start: 43 outliers final: 17 residues processed: 183 average time/residue: 0.5537 time to fit residues: 117.9959 Evaluate side-chains 166 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 210 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 128 optimal weight: 0.0270 chunk 243 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 414 GLN A 532 ASN A 957 GLN B1002 GLN C 207 HIS C 354 ASN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.081062 restraints weight = 29847.182| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.20 r_work: 0.2812 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21679 Z= 0.165 Angle : 0.645 16.588 29560 Z= 0.324 Chirality : 0.048 0.264 3531 Planarity : 0.004 0.040 3708 Dihedral : 5.418 57.546 3669 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.90 % Allowed : 11.21 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2548 helix: 1.66 (0.22), residues: 630 sheet: 0.74 (0.21), residues: 612 loop : -1.60 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.028 0.002 TYR B 904 PHE 0.021 0.002 PHE C 32 TRP 0.007 0.001 TRP A 886 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00397 (21608) covalent geometry : angle 0.62304 (29376) SS BOND : bond 0.00323 ( 29) SS BOND : angle 1.86416 ( 58) hydrogen bonds : bond 0.06610 ( 806) hydrogen bonds : angle 5.00984 ( 2337) link_BETA1-4 : bond 0.00370 ( 14) link_BETA1-4 : angle 1.22543 ( 42) link_NAG-ASN : bond 0.00403 ( 28) link_NAG-ASN : angle 2.75776 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7443 (m-80) cc_final: 0.6514 (m-80) REVERT: A 281 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: A 304 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8311 (mttm) REVERT: A 462 LYS cc_start: 0.8827 (mppt) cc_final: 0.8510 (mppt) REVERT: A 529 LYS cc_start: 0.8412 (mppt) cc_final: 0.8084 (mmmt) REVERT: A 556 ASN cc_start: 0.7774 (t0) cc_final: 0.7421 (t0) REVERT: A 646 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8066 (ttp80) REVERT: A 654 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: A 740 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8510 (ttt) REVERT: B 102 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7265 (mmm-85) REVERT: B 314 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: B 529 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7758 (mttm) REVERT: B 581 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (p) REVERT: B 809 PRO cc_start: 0.7091 (Cg_endo) cc_final: 0.6744 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8673 (mp0) cc_final: 0.8145 (mp0) REVERT: C 556 ASN cc_start: 0.8288 (m-40) cc_final: 0.8038 (m-40) REVERT: C 560 LEU cc_start: 0.7987 (mt) cc_final: 0.7503 (mp) REVERT: C 794 ILE cc_start: 0.8041 (mm) cc_final: 0.7497 (pp) REVERT: C 855 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6931 (m-80) outliers start: 44 outliers final: 20 residues processed: 179 average time/residue: 0.5432 time to fit residues: 113.0035 Evaluate side-chains 168 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 145 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B1002 GLN C 207 HIS C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083286 restraints weight = 30013.381| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.23 r_work: 0.2854 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21679 Z= 0.117 Angle : 0.600 16.124 29560 Z= 0.298 Chirality : 0.045 0.254 3531 Planarity : 0.004 0.039 3708 Dihedral : 5.188 56.344 3669 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.47 % Allowed : 11.51 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2548 helix: 1.77 (0.21), residues: 636 sheet: 0.81 (0.21), residues: 620 loop : -1.49 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.024 0.001 TYR A 170 PHE 0.030 0.001 PHE A 168 TRP 0.009 0.001 TRP B 886 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00258 (21608) covalent geometry : angle 0.58032 (29376) SS BOND : bond 0.00254 ( 29) SS BOND : angle 1.27946 ( 58) hydrogen bonds : bond 0.05377 ( 806) hydrogen bonds : angle 4.85828 ( 2337) link_BETA1-4 : bond 0.00424 ( 14) link_BETA1-4 : angle 1.14087 ( 42) link_NAG-ASN : bond 0.00397 ( 28) link_NAG-ASN : angle 2.66699 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7283 (mmp-170) cc_final: 0.6971 (mmp80) REVERT: A 200 TYR cc_start: 0.7395 (m-80) cc_final: 0.6502 (m-80) REVERT: A 281 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: A 304 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8306 (mttm) REVERT: A 462 LYS cc_start: 0.8836 (mppt) cc_final: 0.8521 (mppt) REVERT: A 529 LYS cc_start: 0.8401 (mppt) cc_final: 0.8069 (mmmt) REVERT: A 556 ASN cc_start: 0.7767 (t0) cc_final: 0.7414 (t0) REVERT: A 646 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7998 (ttp80) REVERT: A 654 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 740 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8191 (ttp) REVERT: B 102 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.7217 (mmm-85) REVERT: B 314 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: B 529 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7742 (mttm) REVERT: B 581 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7606 (p) REVERT: B 809 PRO cc_start: 0.7160 (Cg_endo) cc_final: 0.6794 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8670 (mp0) cc_final: 0.8145 (mp0) REVERT: C 556 ASN cc_start: 0.8293 (m-40) cc_final: 0.8039 (m-40) REVERT: C 560 LEU cc_start: 0.7973 (mt) cc_final: 0.7498 (mp) REVERT: C 794 ILE cc_start: 0.7913 (mm) cc_final: 0.7357 (pp) REVERT: C 855 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6890 (m-80) outliers start: 34 outliers final: 17 residues processed: 168 average time/residue: 0.5579 time to fit residues: 108.6719 Evaluate side-chains 160 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 220 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN C 207 HIS C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082071 restraints weight = 30029.340| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.23 r_work: 0.2833 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 21679 Z= 0.147 Angle : 0.622 16.137 29560 Z= 0.311 Chirality : 0.046 0.259 3531 Planarity : 0.004 0.040 3708 Dihedral : 5.208 56.887 3669 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.68 % Allowed : 11.38 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2548 helix: 1.77 (0.22), residues: 629 sheet: 0.86 (0.21), residues: 614 loop : -1.53 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.025 0.001 TYR A 453 PHE 0.056 0.001 PHE A 168 TRP 0.007 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (21608) covalent geometry : angle 0.60181 (29376) SS BOND : bond 0.00357 ( 29) SS BOND : angle 1.57330 ( 58) hydrogen bonds : bond 0.05991 ( 806) hydrogen bonds : angle 4.90855 ( 2337) link_BETA1-4 : bond 0.00386 ( 14) link_BETA1-4 : angle 1.17498 ( 42) link_NAG-ASN : bond 0.00385 ( 28) link_NAG-ASN : angle 2.67171 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9014.22 seconds wall clock time: 153 minutes 42.63 seconds (9222.63 seconds total)