Starting phenix.real_space_refine on Sun Jul 5 02:09:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp1_26045/07_2026/7tp1_26045.cif" } resolution = 3.81 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= 0.128 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 15679 2.51 5 N 4030 2.21 5 O 4832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24646 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7916 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 7 Chain: "B" 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: "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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 5.99, per 1000 atoms: 0.24 Number of scatterers: 24646 At special positions: 0 Unit cell: (128.52, 133.92, 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 4832 8.00 N 4030 7.00 C 15679 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.01 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 44 sheets defined 27.8% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 4.081A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.079A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.026A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.517A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.576A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.663A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.805A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.630A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.999A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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 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: 3.835A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.062A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.862A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 625 through 630 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.844A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.065A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.620A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.672A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.531A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.796A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.139A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 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 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.133A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.219A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.945A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.786A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.069A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.776A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.643A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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: 3.807A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.270A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.108A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.831A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.920A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.297A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.354A 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: 4.988A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.597A 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: 6.729A 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: 4.440A 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 655 removed outlier: 6.583A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.528A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (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 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.971A 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: 8.520A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.657A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.667A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.773A 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: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.244A 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: 5.003A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.731A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 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: 6.164A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.845A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.738A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.738A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (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 1125 removed outlier: 4.811A 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: 8.632A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.783A 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: 3.999A 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: 6.761A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.438A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.727A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.480A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.480A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (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 1122 1042 hydrogen bonds defined for protein. 2814 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: 6.67 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7327 1.34 - 1.46: 4414 1.46 - 1.58: 13311 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 25181 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.46e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 25176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 32394 3.39 - 6.78: 1830 6.78 - 10.17: 29 10.17 - 13.56: 3 13.56 - 16.95: 1 Bond angle restraints: 34257 Sorted by residual: angle pdb=" CA VAL A 622 " pdb=" CB VAL A 622 " pdb=" CG1 VAL A 622 " ideal model delta sigma weight residual 110.40 127.35 -16.95 1.70e+00 3.46e-01 9.94e+01 angle pdb=" N CYS C 131 " pdb=" CA CYS C 131 " pdb=" C CYS C 131 " ideal model delta sigma weight residual 110.33 120.56 -10.23 1.29e+00 6.01e-01 6.29e+01 angle pdb=" CA PHE C 347 " pdb=" CB PHE C 347 " pdb=" CG PHE C 347 " ideal model delta sigma weight residual 113.80 120.16 -6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" CA THR B 630 " pdb=" CB THR B 630 " pdb=" CG2 THR B 630 " ideal model delta sigma weight residual 110.50 121.22 -10.72 1.70e+00 3.46e-01 3.98e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 118.08 -9.12 1.49e+00 4.50e-01 3.74e+01 ... (remaining 34252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13414 17.93 - 35.87: 863 35.87 - 53.80: 140 53.80 - 71.74: 56 71.74 - 89.67: 33 Dihedral angle restraints: 14506 sinusoidal: 5643 harmonic: 8863 Sorted by residual: 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 -154.57 68.57 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 153.69 -60.69 1 1.00e+01 1.00e-02 4.90e+01 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 -146.58 60.58 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 14503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 4059 0.283 - 0.565: 21 0.565 - 0.848: 0 0.848 - 1.130: 0 1.130 - 1.413: 1 Chirality restraints: 4081 Sorted by residual: 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 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.46e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.24e+01 ... (remaining 4078 not shown) Planarity restraints: 4396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.144 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN C 165 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.135 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" CG ASN B 122 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.236 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.138 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN C 603 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " 0.230 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.180 2.00e-02 2.50e+03 ... (remaining 4393 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 13077 3.00 - 3.47: 24638 3.47 - 3.95: 40710 3.95 - 4.42: 45211 4.42 - 4.90: 74619 Nonbonded interactions: 198255 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.523 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.547 3.040 nonbonded pdb=" OG SER B 746 " pdb=" OE1 GLU B 748 " model vdw 2.556 3.040 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.557 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.560 3.040 ... (remaining 198250 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 635 through 1311)) selection = (chain 'B' and (resid 27 through 623 or resid 635 through 1311)) selection = chain 'C' } 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.010 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 25281 Z= 0.758 Angle : 1.779 16.948 34518 Z= 1.158 Chirality : 0.101 1.413 4081 Planarity : 0.015 0.163 4349 Dihedral : 13.731 89.672 8681 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.73 % Favored : 92.40 % Rotamer: Outliers : 1.39 % Allowed : 3.42 % Favored : 95.19 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.32 (0.14), residues: 3000 helix: -0.58 (0.17), residues: 691 sheet: 0.25 (0.22), residues: 481 loop : -1.35 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1107 TYR 0.162 0.021 TYR B 495 PHE 0.077 0.013 PHE C 59 TRP 0.122 0.021 TRP B 886 HIS 0.017 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01352 / 0.76 (25181) covalent geometry : angle 1.75243 / 1.16 (34257) SS BOND : bond 0.01057 / 0.62 ( 39) SS BOND : angle 2.04308 / 1.24 ( 78) hydrogen bonds : bond 0.17242 / 11.00 ( 1011) hydrogen bonds : angle 8.65739 / 5.96 ( 2814) link_BETA1-4 : bond 0.02289 / 1.35 ( 14) link_BETA1-4 : angle 4.77011 / 2.91 ( 42) link_NAG-ASN : bond 0.00912 / 0.59 ( 47) link_NAG-ASN : angle 4.46932 / 3.00 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6631 (p) REVERT: A 990 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 458 LYS cc_start: 0.9473 (mttt) cc_final: 0.9213 (tptp) REVERT: B 740 MET cc_start: 0.7939 (ttt) cc_final: 0.7414 (tpp) REVERT: C 342 PHE cc_start: 0.9067 (m-80) cc_final: 0.8853 (m-80) outliers start: 37 outliers final: 10 residues processed: 96 average time/residue: 0.1830 time to fit residues: 28.2694 Evaluate side-chains 48 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 328 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN A 655 HIS B 493 GLN B 613 GLN B 628 GLN C 422 ASN C 751 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.045994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.033761 restraints weight = 219372.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034917 restraints weight = 113700.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035316 restraints weight = 63375.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035418 restraints weight = 52369.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035422 restraints weight = 49080.231| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25281 Z= 0.216 Angle : 0.792 12.551 34518 Z= 0.401 Chirality : 0.048 0.411 4081 Planarity : 0.004 0.049 4349 Dihedral : 7.117 58.301 3277 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.33 % Favored : 95.40 % Rotamer: Outliers : 1.20 % Allowed : 4.81 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.55 (0.15), residues: 3000 helix: 1.18 (0.19), residues: 674 sheet: -0.21 (0.19), residues: 651 loop : -1.09 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1019 TYR 0.020 0.002 TYR C 489 PHE 0.018 0.002 PHE B 392 TRP 0.017 0.002 TRP C 64 HIS 0.007 0.002 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (25181) covalent geometry : angle 0.75381 / 0.39 (34257) SS BOND : bond 0.00720 / 0.51 ( 39) SS BOND : angle 2.02700 / 1.21 ( 78) hydrogen bonds : bond 0.05465 / 3.44 ( 1011) hydrogen bonds : angle 6.37561 / 4.36 ( 2814) link_BETA1-4 : bond 0.00461 / 0.25 ( 14) link_BETA1-4 : angle 1.95478 / 1.19 ( 42) link_NAG-ASN : bond 0.00441 / 0.29 ( 47) link_NAG-ASN : angle 3.50247 / 2.30 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: A 987 VAL cc_start: 0.8699 (p) cc_final: 0.8284 (m) REVERT: A 988 GLU cc_start: 0.8718 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 458 LYS cc_start: 0.9568 (mttt) cc_final: 0.9210 (tptp) REVERT: B 625 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6764 (t-170) REVERT: B 740 MET cc_start: 0.7738 (ttt) cc_final: 0.7516 (tpp) REVERT: C 342 PHE cc_start: 0.9089 (m-80) cc_final: 0.8735 (m-80) REVERT: C 740 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8830 (ttp) outliers start: 32 outliers final: 11 residues processed: 70 average time/residue: 0.1411 time to fit residues: 16.9375 Evaluate side-chains 46 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 17 optimal weight: 20.0000 chunk 243 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 675 GLN C 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.045257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033264 restraints weight = 220532.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034121 restraints weight = 114180.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034238 restraints weight = 68190.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034358 restraints weight = 65555.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.034419 restraints weight = 59475.926| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25281 Z= 0.261 Angle : 0.745 9.923 34518 Z= 0.375 Chirality : 0.047 0.424 4081 Planarity : 0.004 0.050 4349 Dihedral : 6.311 42.313 3264 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer: Outliers : 1.05 % Allowed : 7.25 % Favored : 91.69 % 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: -0.47 (0.15), residues: 3000 helix: 1.27 (0.20), residues: 692 sheet: -0.24 (0.19), residues: 677 loop : -1.04 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1039 TYR 0.026 0.002 TYR C1067 PHE 0.036 0.002 PHE C 392 TRP 0.023 0.002 TRP B 633 HIS 0.007 0.002 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (25181) covalent geometry : angle 0.71832 / 0.37 (34257) SS BOND : bond 0.00468 / 0.27 ( 39) SS BOND : angle 1.40994 / 0.85 ( 78) hydrogen bonds : bond 0.05072 / 3.18 ( 1011) hydrogen bonds : angle 6.12918 / 4.21 ( 2814) link_BETA1-4 : bond 0.00452 / 0.28 ( 14) link_BETA1-4 : angle 1.77141 / 1.10 ( 42) link_NAG-ASN : bond 0.00460 / 0.30 ( 47) link_NAG-ASN : angle 2.89056 / 1.90 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 33 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8728 (tpp) cc_final: 0.8457 (tpp) REVERT: A 988 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 458 LYS cc_start: 0.9531 (mttt) cc_final: 0.9284 (tptp) REVERT: B 625 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6862 (t-170) REVERT: C 342 PHE cc_start: 0.9062 (m-80) cc_final: 0.8728 (m-80) outliers start: 28 outliers final: 14 residues processed: 60 average time/residue: 0.1486 time to fit residues: 15.6284 Evaluate side-chains 46 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 134 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.045373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.032892 restraints weight = 221107.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033755 restraints weight = 113808.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034285 restraints weight = 75604.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034591 restraints weight = 58734.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.034789 restraints weight = 50725.269| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25281 Z= 0.199 Angle : 0.652 9.594 34518 Z= 0.328 Chirality : 0.046 0.357 4081 Planarity : 0.004 0.048 4349 Dihedral : 5.822 41.649 3263 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.83 % Favored : 94.97 % Rotamer: Outliers : 1.20 % Allowed : 7.97 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3000 helix: 1.58 (0.20), residues: 699 sheet: -0.10 (0.20), residues: 620 loop : -1.05 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE C 392 TRP 0.018 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (25181) covalent geometry : angle 0.63045 / 0.32 (34257) SS BOND : bond 0.00432 / 0.25 ( 39) SS BOND : angle 1.17022 / 0.72 ( 78) hydrogen bonds : bond 0.04423 / 2.76 ( 1011) hydrogen bonds : angle 5.80383 / 3.99 ( 2814) link_BETA1-4 : bond 0.00341 / 0.22 ( 14) link_BETA1-4 : angle 1.65136 / 1.07 ( 42) link_NAG-ASN : bond 0.00341 / 0.24 ( 47) link_NAG-ASN : angle 2.45478 / 1.63 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 32 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.4492 (OUTLIER) cc_final: 0.4221 (m-40) REVERT: B 458 LYS cc_start: 0.9512 (mttt) cc_final: 0.9181 (tptp) REVERT: B 985 ASP cc_start: 0.8301 (p0) cc_final: 0.7986 (p0) REVERT: C 342 PHE cc_start: 0.9170 (m-80) cc_final: 0.8963 (m-80) REVERT: C 979 ASP cc_start: 0.8885 (m-30) cc_final: 0.8393 (t0) outliers start: 32 outliers final: 18 residues processed: 62 average time/residue: 0.1417 time to fit residues: 16.1205 Evaluate side-chains 50 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.045636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.033562 restraints weight = 219419.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034295 restraints weight = 116186.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034845 restraints weight = 72661.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034868 restraints weight = 66052.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.034983 restraints weight = 56394.746| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25281 Z= 0.133 Angle : 0.591 12.746 34518 Z= 0.299 Chirality : 0.044 0.341 4081 Planarity : 0.003 0.045 4349 Dihedral : 5.416 41.994 3263 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 1.20 % Allowed : 8.61 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3000 helix: 1.83 (0.20), residues: 698 sheet: 0.02 (0.20), residues: 617 loop : -0.97 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE C 392 TRP 0.019 0.001 TRP B 633 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (25181) covalent geometry : angle 0.56885 / 0.29 (34257) SS BOND : bond 0.00430 / 0.24 ( 39) SS BOND : angle 1.89705 / 1.09 ( 78) hydrogen bonds : bond 0.04052 / 2.52 ( 1011) hydrogen bonds : angle 5.54806 / 3.82 ( 2814) link_BETA1-4 : bond 0.00323 / 0.18 ( 14) link_BETA1-4 : angle 1.55646 / 1.01 ( 42) link_NAG-ASN : bond 0.00178 / 0.12 ( 47) link_NAG-ASN : angle 2.01358 / 1.34 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7998 (pt0) REVERT: B 458 LYS cc_start: 0.9444 (mttt) cc_final: 0.9096 (tptp) REVERT: B 1126 CYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6627 (m) REVERT: C 979 ASP cc_start: 0.8917 (m-30) cc_final: 0.8419 (t0) outliers start: 32 outliers final: 20 residues processed: 66 average time/residue: 0.1598 time to fit residues: 18.7308 Evaluate side-chains 54 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 9 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 55 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.045981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033791 restraints weight = 217002.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034993 restraints weight = 121346.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035275 restraints weight = 68405.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035454 restraints weight = 53799.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035502 restraints weight = 50648.465| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25281 Z= 0.105 Angle : 0.550 9.902 34518 Z= 0.277 Chirality : 0.044 0.333 4081 Planarity : 0.003 0.048 4349 Dihedral : 5.042 43.115 3263 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Rotamer: Outliers : 1.35 % Allowed : 8.72 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3000 helix: 2.19 (0.20), residues: 685 sheet: 0.11 (0.20), residues: 618 loop : -0.82 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.023 0.001 TYR A 473 PHE 0.019 0.001 PHE C 392 TRP 0.019 0.001 TRP B 633 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (25181) covalent geometry : angle 0.52866 / 0.27 (34257) SS BOND : bond 0.00312 / 0.17 ( 39) SS BOND : angle 1.44289 / 0.84 ( 78) hydrogen bonds : bond 0.03599 / 2.24 ( 1011) hydrogen bonds : angle 5.26634 / 3.62 ( 2814) link_BETA1-4 : bond 0.00362 / 0.20 ( 14) link_BETA1-4 : angle 1.48968 / 0.97 ( 42) link_NAG-ASN : bond 0.00184 / 0.13 ( 47) link_NAG-ASN : angle 2.09983 / 1.33 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 39 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8493 (tpp) cc_final: 0.8097 (tpp) REVERT: B 458 LYS cc_start: 0.9435 (mttt) cc_final: 0.9090 (tptp) REVERT: B 633 TRP cc_start: 0.7936 (OUTLIER) cc_final: 0.7578 (m-90) REVERT: B 1126 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6536 (m) REVERT: C 342 PHE cc_start: 0.9121 (m-80) cc_final: 0.8705 (m-80) REVERT: C 979 ASP cc_start: 0.8932 (m-30) cc_final: 0.8472 (t0) REVERT: C 980 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8373 (mp) outliers start: 36 outliers final: 20 residues processed: 73 average time/residue: 0.1444 time to fit residues: 18.3296 Evaluate side-chains 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 980 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 17 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 285 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.046137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.033941 restraints weight = 219479.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035129 restraints weight = 123964.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035447 restraints weight = 69815.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035628 restraints weight = 54312.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035673 restraints weight = 51418.286| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25281 Z= 0.096 Angle : 0.532 9.082 34518 Z= 0.269 Chirality : 0.043 0.328 4081 Planarity : 0.003 0.051 4349 Dihedral : 4.782 44.062 3259 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 1.13 % Allowed : 9.09 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 3000 helix: 2.33 (0.20), residues: 685 sheet: 0.15 (0.20), residues: 626 loop : -0.74 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.017 0.001 TYR B1067 PHE 0.021 0.001 PHE C 392 TRP 0.019 0.001 TRP B 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (25181) covalent geometry : angle 0.51547 / 0.27 (34257) SS BOND : bond 0.00316 / 0.19 ( 39) SS BOND : angle 1.11128 / 0.67 ( 78) hydrogen bonds : bond 0.03431 / 2.13 ( 1011) hydrogen bonds : angle 5.12345 / 3.52 ( 2814) link_BETA1-4 : bond 0.00352 / 0.19 ( 14) link_BETA1-4 : angle 1.46263 / 0.94 ( 42) link_NAG-ASN : bond 0.00161 / 0.10 ( 47) link_NAG-ASN : angle 1.86691 / 1.23 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 35 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9489 (mttt) cc_final: 0.8910 (tptp) REVERT: B 633 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7560 (m-90) REVERT: B 1126 CYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6498 (m) REVERT: C 979 ASP cc_start: 0.8940 (m-30) cc_final: 0.8566 (t0) outliers start: 30 outliers final: 20 residues processed: 63 average time/residue: 0.1476 time to fit residues: 16.6992 Evaluate side-chains 57 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 19 optimal weight: 0.5980 chunk 258 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 46 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.045466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.032990 restraints weight = 219653.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.033866 restraints weight = 114713.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034387 restraints weight = 76042.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034732 restraints weight = 59203.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.034937 restraints weight = 50425.201| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25281 Z= 0.176 Angle : 0.588 11.103 34518 Z= 0.295 Chirality : 0.044 0.349 4081 Planarity : 0.003 0.052 4349 Dihedral : 4.880 45.447 3258 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 0.94 % Allowed : 9.73 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 3000 helix: 2.20 (0.20), residues: 685 sheet: 0.06 (0.20), residues: 643 loop : -0.76 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.023 0.001 TYR A 473 PHE 0.021 0.001 PHE C 392 TRP 0.015 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (25181) covalent geometry : angle 0.56601 / 0.29 (34257) SS BOND : bond 0.00411 / 0.25 ( 39) SS BOND : angle 2.05557 / 1.36 ( 78) hydrogen bonds : bond 0.03874 / 2.41 ( 1011) hydrogen bonds : angle 5.30635 / 3.65 ( 2814) link_BETA1-4 : bond 0.00284 / 0.16 ( 14) link_BETA1-4 : angle 1.55963 / 1.01 ( 42) link_NAG-ASN : bond 0.00269 / 0.17 ( 47) link_NAG-ASN : angle 1.92422 / 1.25 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9496 (mttt) cc_final: 0.9012 (tptp) REVERT: C 979 ASP cc_start: 0.8980 (m-30) cc_final: 0.8579 (t0) outliers start: 25 outliers final: 17 residues processed: 55 average time/residue: 0.1532 time to fit residues: 15.2443 Evaluate side-chains 50 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 418 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 217 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 207 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1036 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.045845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.033384 restraints weight = 218519.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034288 restraints weight = 112213.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.034840 restraints weight = 73386.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035178 restraints weight = 56501.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035346 restraints weight = 48221.399| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25281 Z= 0.111 Angle : 0.543 9.675 34518 Z= 0.274 Chirality : 0.043 0.321 4081 Planarity : 0.003 0.054 4349 Dihedral : 4.721 46.783 3258 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 0.79 % Allowed : 9.88 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 3000 helix: 2.24 (0.20), residues: 693 sheet: 0.13 (0.20), residues: 631 loop : -0.73 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.031 0.001 TYR A 473 PHE 0.019 0.001 PHE C 392 TRP 0.020 0.001 TRP B 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25181) covalent geometry : angle 0.52318 / 0.27 (34257) SS BOND : bond 0.00318 / 0.18 ( 39) SS BOND : angle 1.77606 / 1.16 ( 78) hydrogen bonds : bond 0.03584 / 2.23 ( 1011) hydrogen bonds : angle 5.14871 / 3.54 ( 2814) link_BETA1-4 : bond 0.00345 / 0.19 ( 14) link_BETA1-4 : angle 1.44653 / 0.95 ( 42) link_NAG-ASN : bond 0.00150 / 0.10 ( 47) link_NAG-ASN : angle 1.79433 / 1.20 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8335 (tmm) cc_final: 0.8079 (tmm) REVERT: B 458 LYS cc_start: 0.9511 (mttt) cc_final: 0.8871 (tptp) REVERT: C 979 ASP cc_start: 0.8904 (m-30) cc_final: 0.8554 (t0) outliers start: 21 outliers final: 20 residues processed: 54 average time/residue: 0.1611 time to fit residues: 15.3295 Evaluate side-chains 53 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 56 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.032995 restraints weight = 219195.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033872 restraints weight = 113221.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034420 restraints weight = 74557.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034751 restraints weight = 57537.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034936 restraints weight = 49088.355| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25281 Z= 0.165 Angle : 0.573 9.344 34518 Z= 0.287 Chirality : 0.043 0.337 4081 Planarity : 0.003 0.054 4349 Dihedral : 4.782 47.364 3258 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 0.79 % Allowed : 9.92 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 3000 helix: 2.20 (0.20), residues: 686 sheet: 0.01 (0.19), residues: 663 loop : -0.75 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.032 0.001 TYR A 473 PHE 0.020 0.001 PHE C 392 TRP 0.041 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (25181) covalent geometry : angle 0.55323 / 0.28 (34257) SS BOND : bond 0.00364 / 0.21 ( 39) SS BOND : angle 1.79282 / 1.16 ( 78) hydrogen bonds : bond 0.03785 / 2.36 ( 1011) hydrogen bonds : angle 5.25752 / 3.61 ( 2814) link_BETA1-4 : bond 0.00289 / 0.16 ( 14) link_BETA1-4 : angle 1.53034 / 1.00 ( 42) link_NAG-ASN : bond 0.00244 / 0.15 ( 47) link_NAG-ASN : angle 1.86109 / 1.22 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8478 (tmm) cc_final: 0.8225 (tmm) REVERT: B 458 LYS cc_start: 0.9523 (mttt) cc_final: 0.8867 (tptp) REVERT: C 979 ASP cc_start: 0.8911 (m-30) cc_final: 0.8560 (t0) outliers start: 21 outliers final: 21 residues processed: 54 average time/residue: 0.1320 time to fit residues: 12.8531 Evaluate side-chains 54 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 56 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 271 optimal weight: 0.0020 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN C 239 GLN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.045032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.032541 restraints weight = 221276.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033402 restraints weight = 115348.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.033934 restraints weight = 76424.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.034261 restraints weight = 59255.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034452 restraints weight = 50823.549| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25281 Z= 0.213 Angle : 0.623 9.432 34518 Z= 0.311 Chirality : 0.044 0.339 4081 Planarity : 0.004 0.054 4349 Dihedral : 5.019 48.304 3258 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.83 % Rotamer: Outliers : 0.86 % Allowed : 9.85 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3000 helix: 2.01 (0.20), residues: 683 sheet: -0.06 (0.19), residues: 667 loop : -0.82 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.031 0.001 TYR A 473 PHE 0.022 0.001 PHE C 392 TRP 0.041 0.002 TRP B 633 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (25181) covalent geometry : angle 0.60354 / 0.31 (34257) SS BOND : bond 0.00399 / 0.23 ( 39) SS BOND : angle 1.90157 / 1.22 ( 78) hydrogen bonds : bond 0.04201 / 2.62 ( 1011) hydrogen bonds : angle 5.48670 / 3.77 ( 2814) link_BETA1-4 : bond 0.00283 / 0.17 ( 14) link_BETA1-4 : angle 1.62246 / 1.08 ( 42) link_NAG-ASN : bond 0.00320 / 0.21 ( 47) link_NAG-ASN : angle 1.92790 / 1.25 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.02 seconds wall clock time: 61 minutes 35.52 seconds (3695.52 seconds total)