Starting phenix.real_space_refine on Fri Feb 6 10:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp0_26043/02_2026/7tp0_26043.map" } resolution = 3.57 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= -0.004 sd= 0.138 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 105 5.16 5 C 15641 2.51 5 N 4020 2.21 5 O 4823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24589 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "B" Number of atoms: 7859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7859 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 48, 'TRANS': 958} Chain breaks: 7 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7891 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.11, per 1000 atoms: 0.21 Number of scatterers: 24589 At special positions: 0 Unit cell: (128.52, 142.56, 177.12, 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 105 16.00 O 4823 8.00 N 4020 7.00 C 15641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 852.3 milliseconds 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5696 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.104A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.873A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.899A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 633 through 639 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.941A 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: 4.107A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.599A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.720A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.599A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.532A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 976 through 984 removed outlier: 3.689A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.129A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.045A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.094A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 758 through 783 removed outlier: 3.565A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.896A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.927A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.612A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.974A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.829A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.575A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.683A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.800A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.143A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.545A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.795A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.659A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.768A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.557A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.105A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.864A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.541A 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 removed outlier: 3.755A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.253A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.998A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.807A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.564A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.883A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.592A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.766A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.304A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.117A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.855A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.918A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.001A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.370A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.556A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.825A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.251A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.569A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 4.010A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.046A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.908A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.740A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.011A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.402A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.617A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.636A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1022 hydrogen bonds defined for protein. 2760 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: 5.65 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6768 1.33 - 1.46: 4646 1.46 - 1.58: 13578 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 25121 Sorted by residual: bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.53e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 25116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 33880 4.81 - 9.63: 287 9.63 - 14.44: 6 14.44 - 19.26: 0 19.26 - 24.07: 1 Bond angle restraints: 34174 Sorted by residual: angle pdb=" CA VAL B 622 " pdb=" CB VAL B 622 " pdb=" CG1 VAL B 622 " ideal model delta sigma weight residual 110.40 134.47 -24.07 1.70e+00 3.46e-01 2.01e+02 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 119.56 -10.60 1.49e+00 4.50e-01 5.06e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 109.07 119.45 -10.38 1.52e+00 4.33e-01 4.67e+01 angle pdb=" CA PRO A 631 " pdb=" N PRO A 631 " pdb=" CD PRO A 631 " ideal model delta sigma weight residual 112.00 102.92 9.08 1.40e+00 5.10e-01 4.20e+01 angle pdb=" N ARG B 457 " pdb=" CA ARG B 457 " pdb=" C ARG B 457 " ideal model delta sigma weight residual 111.24 118.23 -6.99 1.29e+00 6.01e-01 2.94e+01 ... (remaining 34169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14588 17.87 - 35.75: 908 35.75 - 53.62: 172 53.62 - 71.50: 58 71.50 - 89.37: 30 Dihedral angle restraints: 15756 sinusoidal: 6912 harmonic: 8844 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.57 71.57 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.59 64.59 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.49 60.49 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 4063 0.314 - 0.629: 9 0.629 - 0.943: 0 0.943 - 1.257: 0 1.257 - 1.572: 1 Chirality restraints: 4073 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.09e+01 ... (remaining 4070 not shown) Planarity restraints: 4387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.141 2.00e-02 2.50e+03 1.48e-01 2.72e+02 pdb=" CG ASN B 657 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.138 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN A1074 " 0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.141 2.00e-02 2.50e+03 1.45e-01 2.63e+02 pdb=" CG ASN B 165 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.173 2.00e-02 2.50e+03 ... (remaining 4384 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 12853 3.00 - 3.48: 23945 3.48 - 3.95: 40143 3.95 - 4.43: 44164 4.43 - 4.90: 74750 Nonbonded interactions: 195855 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.527 3.040 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.530 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.550 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.561 3.040 nonbonded pdb=" OG SER A 746 " pdb=" OE1 GLU A 748 " model vdw 2.562 3.040 ... (remaining 195850 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 623 or resid 639 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 623 or resid 639 through 1311)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.460 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.014 0.079 25221 Z= 0.767 Angle : 1.787 24.073 34435 Z= 1.165 Chirality : 0.102 1.572 4073 Planarity : 0.014 0.207 4340 Dihedral : 13.118 89.372 9943 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.59 % Rotamer: Outliers : 1.62 % Allowed : 3.01 % Favored : 95.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.07 % 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: -1.08 (0.14), residues: 2994 helix: -0.69 (0.17), residues: 689 sheet: 0.47 (0.21), residues: 544 loop : -1.11 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 466 TYR 0.146 0.021 TYR A 904 PHE 0.078 0.011 PHE A 58 TRP 0.201 0.022 TRP C 886 HIS 0.015 0.003 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01356 (25121) covalent geometry : angle 1.75726 (34174) SS BOND : bond 0.01112 ( 39) SS BOND : angle 1.98668 ( 78) hydrogen bonds : bond 0.16198 ( 1018) hydrogen bonds : angle 8.24323 ( 2760) link_BETA1-4 : bond 0.02624 ( 14) link_BETA1-4 : angle 5.41569 ( 42) link_NAG-ASN : bond 0.01004 ( 47) link_NAG-ASN : angle 4.52846 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 56 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7907 (mm) REVERT: B 210 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4869 (mt) REVERT: B 328 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7799 (mmm-85) REVERT: B 455 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5354 (mt) REVERT: C 466 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5890 (tpp80) REVERT: C 869 MET cc_start: 0.8813 (mtt) cc_final: 0.8574 (mtm) outliers start: 43 outliers final: 9 residues processed: 99 average time/residue: 0.1635 time to fit residues: 26.3406 Evaluate side-chains 52 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 625 HIS B 907 ASN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.055125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039069 restraints weight = 144556.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040481 restraints weight = 79386.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040761 restraints weight = 44109.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.041047 restraints weight = 41025.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041103 restraints weight = 36538.424| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 25221 Z= 0.154 Angle : 0.732 14.794 34435 Z= 0.369 Chirality : 0.047 0.268 4073 Planarity : 0.005 0.177 4340 Dihedral : 7.191 59.685 4560 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.97 % Favored : 95.79 % Rotamer: Outliers : 1.02 % Allowed : 4.41 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.38 % 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: -0.24 (0.15), residues: 2994 helix: 1.07 (0.20), residues: 677 sheet: 0.18 (0.18), residues: 694 loop : -0.84 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 319 TYR 0.019 0.002 TYR C 265 PHE 0.016 0.001 PHE C 392 TRP 0.018 0.002 TRP B 64 HIS 0.008 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00341 (25121) covalent geometry : angle 0.67978 (34174) SS BOND : bond 0.00490 ( 39) SS BOND : angle 1.97275 ( 78) hydrogen bonds : bond 0.05040 ( 1018) hydrogen bonds : angle 6.19658 ( 2760) link_BETA1-4 : bond 0.00500 ( 14) link_BETA1-4 : angle 2.94851 ( 42) link_NAG-ASN : bond 0.00392 ( 47) link_NAG-ASN : angle 3.76336 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8543 (ptt-90) REVERT: A 468 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 519 HIS cc_start: 0.6716 (m90) cc_final: 0.6308 (p-80) REVERT: A 779 GLN cc_start: 0.7858 (tp40) cc_final: 0.7248 (mm110) REVERT: B 122 ASN cc_start: 0.2375 (OUTLIER) cc_final: 0.2068 (p0) REVERT: B 210 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.5207 (mt) REVERT: B 455 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6135 (mt) REVERT: B 731 MET cc_start: 0.9207 (ptt) cc_final: 0.8857 (ptm) REVERT: C 456 PHE cc_start: 0.8293 (m-80) cc_final: 0.8044 (m-80) REVERT: C 869 MET cc_start: 0.8607 (mtt) cc_final: 0.8294 (mtm) REVERT: C 902 MET cc_start: 0.9249 (mmm) cc_final: 0.9037 (tpt) outliers start: 27 outliers final: 8 residues processed: 70 average time/residue: 0.1656 time to fit residues: 19.6689 Evaluate side-chains 50 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 7 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 174 optimal weight: 0.0060 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 625 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.053919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037789 restraints weight = 144586.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039125 restraints weight = 80429.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039348 restraints weight = 44773.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.039810 restraints weight = 41924.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039841 restraints weight = 37040.321| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25221 Z= 0.227 Angle : 0.691 12.372 34435 Z= 0.347 Chirality : 0.046 0.233 4073 Planarity : 0.005 0.165 4340 Dihedral : 6.628 60.934 4548 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.91 % Favored : 94.86 % Rotamer: Outliers : 1.39 % Allowed : 5.01 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.16 (0.15), residues: 2994 helix: 1.17 (0.20), residues: 697 sheet: 0.20 (0.19), residues: 675 loop : -0.80 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 328 TYR 0.021 0.002 TYR A1067 PHE 0.014 0.002 PHE A 275 TRP 0.015 0.002 TRP C 886 HIS 0.010 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00534 (25121) covalent geometry : angle 0.65575 (34174) SS BOND : bond 0.00500 ( 39) SS BOND : angle 1.29828 ( 78) hydrogen bonds : bond 0.04797 ( 1018) hydrogen bonds : angle 5.92514 ( 2760) link_BETA1-4 : bond 0.00555 ( 14) link_BETA1-4 : angle 2.96731 ( 42) link_NAG-ASN : bond 0.00399 ( 47) link_NAG-ASN : angle 2.97796 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 39 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.3032 (OUTLIER) cc_final: 0.2830 (pm20) REVERT: A 408 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8569 (ptt-90) REVERT: A 468 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 519 HIS cc_start: 0.6736 (m90) cc_final: 0.6398 (p-80) REVERT: B 122 ASN cc_start: 0.2559 (OUTLIER) cc_final: 0.2188 (p0) REVERT: B 210 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5349 (mt) REVERT: C 165 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.6722 (p0) REVERT: C 456 PHE cc_start: 0.8303 (m-80) cc_final: 0.8103 (m-80) REVERT: C 902 MET cc_start: 0.9284 (mmm) cc_final: 0.9033 (tpt) outliers start: 37 outliers final: 13 residues processed: 74 average time/residue: 0.1517 time to fit residues: 19.1546 Evaluate side-chains 54 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 274 optimal weight: 0.0980 chunk 199 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 69 optimal weight: 0.0870 chunk 210 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.054833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038835 restraints weight = 143271.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040250 restraints weight = 78959.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.040568 restraints weight = 43237.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040871 restraints weight = 40108.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040913 restraints weight = 36056.532| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 25221 Z= 0.109 Angle : 0.583 11.636 34435 Z= 0.296 Chirality : 0.044 0.257 4073 Planarity : 0.004 0.156 4340 Dihedral : 6.023 64.364 4546 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.71 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 6.14 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.13 (0.15), residues: 2994 helix: 1.61 (0.20), residues: 693 sheet: 0.29 (0.19), residues: 700 loop : -0.67 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.020 0.001 TYR B 265 PHE 0.019 0.001 PHE B 65 TRP 0.012 0.001 TRP C 436 HIS 0.009 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00235 (25121) covalent geometry : angle 0.54900 (34174) SS BOND : bond 0.00504 ( 39) SS BOND : angle 2.13749 ( 78) hydrogen bonds : bond 0.03847 ( 1018) hydrogen bonds : angle 5.56888 ( 2760) link_BETA1-4 : bond 0.00709 ( 14) link_BETA1-4 : angle 2.56970 ( 42) link_NAG-ASN : bond 0.00234 ( 47) link_NAG-ASN : angle 2.36485 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 1.048 Fit side-chains REVERT: A 468 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 519 HIS cc_start: 0.6600 (m90) cc_final: 0.6320 (p-80) REVERT: B 122 ASN cc_start: 0.2302 (OUTLIER) cc_final: 0.1964 (p0) REVERT: B 1029 MET cc_start: 0.9047 (tpp) cc_final: 0.8560 (ttm) REVERT: C 165 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.6737 (p0) REVERT: C 456 PHE cc_start: 0.8205 (m-80) cc_final: 0.7979 (m-80) REVERT: C 902 MET cc_start: 0.9284 (mmm) cc_final: 0.9058 (tpt) outliers start: 25 outliers final: 12 residues processed: 59 average time/residue: 0.1579 time to fit residues: 16.5875 Evaluate side-chains 49 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 174 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS B 99 ASN B 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.054650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038662 restraints weight = 144180.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.040105 restraints weight = 80189.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.040303 restraints weight = 44332.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040526 restraints weight = 43504.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040578 restraints weight = 38734.001| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 25221 Z= 0.148 Angle : 0.580 11.875 34435 Z= 0.292 Chirality : 0.044 0.258 4073 Planarity : 0.004 0.153 4340 Dihedral : 5.793 67.727 4544 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 0.90 % Allowed : 6.67 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.17 (0.15), residues: 2994 helix: 1.63 (0.20), residues: 702 sheet: 0.30 (0.18), residues: 716 loop : -0.65 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE B 65 TRP 0.011 0.001 TRP C 436 HIS 0.008 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00347 (25121) covalent geometry : angle 0.55275 (34174) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.49787 ( 78) hydrogen bonds : bond 0.03904 ( 1018) hydrogen bonds : angle 5.46637 ( 2760) link_BETA1-4 : bond 0.00580 ( 14) link_BETA1-4 : angle 2.68877 ( 42) link_NAG-ASN : bond 0.00220 ( 47) link_NAG-ASN : angle 2.19480 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 35 time to evaluate : 0.859 Fit side-chains REVERT: A 468 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7843 (mm) REVERT: A 519 HIS cc_start: 0.6639 (m90) cc_final: 0.6368 (p-80) REVERT: B 731 MET cc_start: 0.9028 (ptm) cc_final: 0.8818 (ptm) REVERT: B 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8649 (ttm) REVERT: C 165 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6945 (p0) REVERT: C 456 PHE cc_start: 0.8281 (m-80) cc_final: 0.8062 (m-80) REVERT: C 902 MET cc_start: 0.9280 (mmm) cc_final: 0.9049 (tpt) outliers start: 24 outliers final: 15 residues processed: 55 average time/residue: 0.1424 time to fit residues: 14.1981 Evaluate side-chains 51 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 675 GLN A1088 HIS B 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.054865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038895 restraints weight = 144455.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040336 restraints weight = 79998.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040558 restraints weight = 44347.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040750 restraints weight = 42658.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040811 restraints weight = 38826.726| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 25221 Z= 0.121 Angle : 0.536 11.734 34435 Z= 0.272 Chirality : 0.043 0.259 4073 Planarity : 0.004 0.151 4340 Dihedral : 5.505 69.983 4542 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 1.05 % Allowed : 7.08 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2994 helix: 1.83 (0.20), residues: 690 sheet: 0.41 (0.19), residues: 696 loop : -0.62 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE B 65 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00277 (25121) covalent geometry : angle 0.51346 (34174) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.18938 ( 78) hydrogen bonds : bond 0.03650 ( 1018) hydrogen bonds : angle 5.30768 ( 2760) link_BETA1-4 : bond 0.00618 ( 14) link_BETA1-4 : angle 2.53044 ( 42) link_NAG-ASN : bond 0.00164 ( 47) link_NAG-ASN : angle 1.88190 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 36 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7907 (mm) REVERT: A 519 HIS cc_start: 0.6574 (m90) cc_final: 0.6305 (p-80) REVERT: B 122 ASN cc_start: 0.2349 (OUTLIER) cc_final: 0.2056 (p0) REVERT: B 985 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: B 1029 MET cc_start: 0.9121 (tpp) cc_final: 0.8688 (ttm) REVERT: C 165 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.6723 (p0) REVERT: C 456 PHE cc_start: 0.8277 (m-80) cc_final: 0.8077 (m-80) REVERT: C 902 MET cc_start: 0.9281 (mmm) cc_final: 0.9035 (tpt) outliers start: 28 outliers final: 14 residues processed: 60 average time/residue: 0.1387 time to fit residues: 15.0727 Evaluate side-chains 52 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 114 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 130 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.054816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.038836 restraints weight = 144331.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040273 restraints weight = 79889.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040509 restraints weight = 44230.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.040695 restraints weight = 42629.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040760 restraints weight = 38607.495| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25221 Z= 0.122 Angle : 0.537 11.775 34435 Z= 0.269 Chirality : 0.043 0.254 4073 Planarity : 0.004 0.150 4340 Dihedral : 5.316 70.468 4542 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 0.98 % Allowed : 7.38 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.34 (0.15), residues: 2994 helix: 1.87 (0.20), residues: 690 sheet: 0.45 (0.19), residues: 696 loop : -0.59 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.001 PHE A 486 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00282 (25121) covalent geometry : angle 0.51587 (34174) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.16926 ( 78) hydrogen bonds : bond 0.03604 ( 1018) hydrogen bonds : angle 5.23066 ( 2760) link_BETA1-4 : bond 0.00615 ( 14) link_BETA1-4 : angle 2.56045 ( 42) link_NAG-ASN : bond 0.00160 ( 47) link_NAG-ASN : angle 1.79291 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7856 (mm) REVERT: A 519 HIS cc_start: 0.6662 (m90) cc_final: 0.6412 (p-80) REVERT: B 985 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: B 1029 MET cc_start: 0.9130 (tpp) cc_final: 0.8681 (ttm) REVERT: C 165 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.6811 (p0) REVERT: C 456 PHE cc_start: 0.8282 (m-80) cc_final: 0.8076 (m-80) REVERT: C 902 MET cc_start: 0.9274 (mmm) cc_final: 0.9027 (tpt) outliers start: 26 outliers final: 20 residues processed: 61 average time/residue: 0.1379 time to fit residues: 15.3848 Evaluate side-chains 57 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 140 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 287 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038181 restraints weight = 144791.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039620 restraints weight = 80528.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.039787 restraints weight = 44738.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039994 restraints weight = 43955.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040045 restraints weight = 39364.002| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25221 Z= 0.191 Angle : 0.572 11.918 34435 Z= 0.288 Chirality : 0.044 0.251 4073 Planarity : 0.004 0.150 4340 Dihedral : 5.441 70.151 4542 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 1.02 % Allowed : 7.65 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.24 (0.15), residues: 2994 helix: 1.76 (0.20), residues: 694 sheet: 0.30 (0.18), residues: 720 loop : -0.63 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE C 392 TRP 0.008 0.001 TRP C 436 HIS 0.036 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00448 (25121) covalent geometry : angle 0.55141 (34174) SS BOND : bond 0.00436 ( 39) SS BOND : angle 1.22158 ( 78) hydrogen bonds : bond 0.03944 ( 1018) hydrogen bonds : angle 5.36152 ( 2760) link_BETA1-4 : bond 0.00601 ( 14) link_BETA1-4 : angle 2.62783 ( 42) link_NAG-ASN : bond 0.00229 ( 47) link_NAG-ASN : angle 1.84440 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 519 HIS cc_start: 0.6649 (m90) cc_final: 0.6420 (p90) REVERT: B 985 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: B 1029 MET cc_start: 0.9127 (tpp) cc_final: 0.8694 (ttm) REVERT: C 165 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6828 (p0) REVERT: C 902 MET cc_start: 0.9276 (mmm) cc_final: 0.9036 (tpt) outliers start: 27 outliers final: 22 residues processed: 58 average time/residue: 0.1477 time to fit residues: 15.6177 Evaluate side-chains 59 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 165 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.054637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038612 restraints weight = 145049.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.040110 restraints weight = 80335.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040302 restraints weight = 43951.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040450 restraints weight = 41431.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040540 restraints weight = 39225.662| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 25221 Z= 0.129 Angle : 0.529 11.609 34435 Z= 0.267 Chirality : 0.043 0.248 4073 Planarity : 0.004 0.149 4340 Dihedral : 5.303 71.465 4542 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 1.13 % Allowed : 7.72 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.33 (0.15), residues: 2994 helix: 1.86 (0.20), residues: 693 sheet: 0.42 (0.19), residues: 701 loop : -0.60 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.017 0.001 TYR A1067 PHE 0.035 0.001 PHE C 392 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00299 (25121) covalent geometry : angle 0.50884 (34174) SS BOND : bond 0.00402 ( 39) SS BOND : angle 1.14798 ( 78) hydrogen bonds : bond 0.03651 ( 1018) hydrogen bonds : angle 5.24122 ( 2760) link_BETA1-4 : bond 0.00616 ( 14) link_BETA1-4 : angle 2.48042 ( 42) link_NAG-ASN : bond 0.00154 ( 47) link_NAG-ASN : angle 1.71563 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 35 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8444 (pt) REVERT: A 468 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 519 HIS cc_start: 0.6667 (m90) cc_final: 0.6431 (p90) REVERT: B 985 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: B 1029 MET cc_start: 0.9106 (tpp) cc_final: 0.8679 (ttm) REVERT: C 165 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.6886 (p0) REVERT: C 902 MET cc_start: 0.9287 (mmm) cc_final: 0.9041 (tpt) outliers start: 30 outliers final: 22 residues processed: 62 average time/residue: 0.1398 time to fit residues: 15.6795 Evaluate side-chains 60 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 47 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 174 optimal weight: 0.0670 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN C1125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.054860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038873 restraints weight = 144261.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040263 restraints weight = 80037.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040449 restraints weight = 44765.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040823 restraints weight = 42736.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.040850 restraints weight = 38586.510| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 25221 Z= 0.111 Angle : 0.512 11.535 34435 Z= 0.259 Chirality : 0.043 0.246 4073 Planarity : 0.004 0.149 4340 Dihedral : 5.131 72.222 4542 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 1.02 % Allowed : 7.98 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2994 helix: 1.93 (0.20), residues: 693 sheet: 0.50 (0.19), residues: 693 loop : -0.57 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 634 TYR 0.017 0.001 TYR A1067 PHE 0.028 0.001 PHE C 392 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00257 (25121) covalent geometry : angle 0.49281 (34174) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.09636 ( 78) hydrogen bonds : bond 0.03473 ( 1018) hydrogen bonds : angle 5.14156 ( 2760) link_BETA1-4 : bond 0.00596 ( 14) link_BETA1-4 : angle 2.44508 ( 42) link_NAG-ASN : bond 0.00141 ( 47) link_NAG-ASN : angle 1.62474 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8426 (pt) REVERT: A 468 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7822 (mm) REVERT: A 519 HIS cc_start: 0.6610 (m90) cc_final: 0.6371 (p90) REVERT: B 985 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: B 1029 MET cc_start: 0.9103 (tpp) cc_final: 0.8683 (ttm) REVERT: C 165 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.6833 (p0) REVERT: C 902 MET cc_start: 0.9288 (mmm) cc_final: 0.9040 (tpt) outliers start: 27 outliers final: 22 residues processed: 58 average time/residue: 0.1314 time to fit residues: 14.0297 Evaluate side-chains 60 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 148 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 131 optimal weight: 0.0570 chunk 14 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.053998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.037838 restraints weight = 145529.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.039236 restraints weight = 81899.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039366 restraints weight = 45581.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.039617 restraints weight = 44519.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039656 restraints weight = 40617.764| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25221 Z= 0.212 Angle : 0.589 11.864 34435 Z= 0.297 Chirality : 0.044 0.242 4073 Planarity : 0.004 0.149 4340 Dihedral : 5.474 70.494 4542 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.11 % Favored : 94.72 % Rotamer: Outliers : 1.05 % Allowed : 8.06 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: 0.21 (0.15), residues: 2994 helix: 1.68 (0.20), residues: 703 sheet: 0.32 (0.19), residues: 712 loop : -0.63 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.020 0.001 TYR A1067 PHE 0.029 0.002 PHE C 392 TRP 0.008 0.001 TRP A 886 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00495 (25121) covalent geometry : angle 0.56918 (34174) SS BOND : bond 0.00451 ( 39) SS BOND : angle 1.29138 ( 78) hydrogen bonds : bond 0.04145 ( 1018) hydrogen bonds : angle 5.40778 ( 2760) link_BETA1-4 : bond 0.00556 ( 14) link_BETA1-4 : angle 2.64380 ( 42) link_NAG-ASN : bond 0.00273 ( 47) link_NAG-ASN : angle 1.80352 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.41 seconds wall clock time: 57 minutes 41.26 seconds (3461.26 seconds total)