Starting phenix.real_space_refine on Sun Jul 5 01:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tox_26040/07_2026/7tox_26040.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15662 2.51 5 N 4026 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24618 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7923 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "B" Number of atoms: 7923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7923 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "C" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7918 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} 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: 5.31, per 1000 atoms: 0.22 Number of scatterers: 24618 At special positions: 0 Unit cell: (133.92, 135, 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 4825 8.00 N 4026 7.00 C 15662 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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: 2.18 Conformation dependent library (CDL) restraints added in 903.2 milliseconds 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 46 sheets defined 27.5% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.646A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.547A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.618A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.368A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 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: 4.237A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.075A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.561A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.675A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.584A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.937A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.834A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.848A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.968A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.565A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.855A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.573A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.846A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.584A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.665A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.803A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.037A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.708A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) 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 removed outlier: 3.802A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.048A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.707A 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 616 through 620 Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.090A 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 removed outlier: 3.600A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.648A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.715A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (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: 3.601A 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: 3.861A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.867A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.136A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.812A 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: 3.686A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.421A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.703A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.201A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.259A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.689A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.641A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.165A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.126A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.887A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.940A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.760A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.497A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC4, 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: 7.072A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.575A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.719A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.719A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.652A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.961A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.594A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.604A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.555A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.324A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.761A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.497A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.564A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.998A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.707A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.632A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.632A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.857A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2793 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: 6.10 Time building geometry restraints manager: 2.91 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: 7297 1.34 - 1.46: 4492 1.46 - 1.58: 13234 1.58 - 1.71: 0 1.71 - 1.83: 129 Bond restraints: 25152 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.489 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 25147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 32988 3.69 - 7.39: 1215 7.39 - 11.08: 10 11.08 - 14.78: 1 14.78 - 18.47: 1 Bond angle restraints: 34215 Sorted by residual: angle pdb=" CA VAL C 622 " pdb=" CB VAL C 622 " pdb=" CG1 VAL C 622 " ideal model delta sigma weight residual 110.40 128.87 -18.47 1.70e+00 3.46e-01 1.18e+02 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 119.71 -10.64 1.52e+00 4.33e-01 4.90e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 118.78 -9.82 1.49e+00 4.50e-01 4.34e+01 angle pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " pdb=" CG PHE B 456 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 34210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13391 17.96 - 35.92: 849 35.92 - 53.88: 155 53.88 - 71.84: 53 71.84 - 89.79: 36 Dihedral angle restraints: 14484 sinusoidal: 5637 harmonic: 8847 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 -166.03 80.03 1 1.00e+01 1.00e-02 7.94e+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 -154.65 68.65 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CA LEU A 110 " pdb=" C LEU A 110 " pdb=" N ASP A 111 " pdb=" CA ASP A 111 " ideal model delta harmonic sigma weight residual -180.00 -149.99 -30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 4058 0.289 - 0.578: 16 0.578 - 0.867: 0 0.867 - 1.155: 0 1.155 - 1.444: 1 Chirality restraints: 4075 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 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 8.20e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 ... (remaining 4072 not shown) Planarity restraints: 4388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.139 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN C 165 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.221 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.135 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" CG ASN C1074 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.223 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.140 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN B 165 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.213 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " -0.174 2.00e-02 2.50e+03 ... (remaining 4385 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12550 2.99 - 3.47: 23906 3.47 - 3.95: 40442 3.95 - 4.42: 44404 4.42 - 4.90: 74869 Nonbonded interactions: 196171 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.515 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.523 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.524 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.550 3.040 ... (remaining 196166 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 622 or resid 632 through 1311)) selection = (chain 'B' and (resid 27 through 622 or resid 632 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: 2.090 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.750 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.080 25252 Z= 0.767 Angle : 1.783 18.471 34476 Z= 1.167 Chirality : 0.101 1.444 4075 Planarity : 0.014 0.169 4341 Dihedral : 13.688 89.795 8669 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.68 % Favored : 92.78 % Rotamer: Outliers : 1.35 % Allowed : 3.16 % Favored : 95.49 % Cbeta Deviations : 0.04 % 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: -1.12 (0.14), residues: 2993 helix: -0.71 (0.17), residues: 682 sheet: 0.39 (0.22), residues: 501 loop : -1.09 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 466 TYR 0.188 0.020 TYR C 495 PHE 0.060 0.011 PHE C 497 TRP 0.131 0.021 TRP B 353 HIS 0.014 0.003 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01358 / 0.77 (25152) covalent geometry : angle 1.75514 / 1.17 (34215) SS BOND : bond 0.01229 / 0.70 ( 39) SS BOND : angle 2.10724 / 1.36 ( 78) hydrogen bonds : bond 0.16133 / 10.51 ( 1016) hydrogen bonds : angle 8.37931 / 5.79 ( 2793) link_BETA1-4 : bond 0.02640 / 1.48 ( 14) link_BETA1-4 : angle 4.76214 / 3.07 ( 42) link_NAG-ASN : bond 0.01083 / 0.70 ( 47) link_NAG-ASN : angle 4.49992 / 2.96 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 764 ASN cc_start: 0.8253 (m-40) cc_final: 0.8043 (t0) REVERT: C 474 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6513 (mp10) outliers start: 36 outliers final: 9 residues processed: 89 average time/residue: 0.1801 time to fit residues: 26.1156 Evaluate side-chains 44 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 641 ASN C 751 ASN C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.054300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039464 restraints weight = 156071.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040522 restraints weight = 96184.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.040825 restraints weight = 57616.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041012 restraints weight = 54875.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041025 restraints weight = 47237.193| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25252 Z= 0.170 Angle : 0.732 13.688 34476 Z= 0.372 Chirality : 0.047 0.284 4075 Planarity : 0.004 0.046 4341 Dihedral : 6.798 78.261 3271 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.37 % Favored : 96.46 % Rotamer: Outliers : 1.05 % Allowed : 4.97 % Favored : 93.98 % 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: -0.28 (0.15), residues: 2993 helix: 1.11 (0.20), residues: 680 sheet: -0.04 (0.20), residues: 621 loop : -0.77 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1019 TYR 0.020 0.002 TYR C 495 PHE 0.014 0.002 PHE C 817 TRP 0.017 0.002 TRP C 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (25152) covalent geometry : angle 0.69061 / 0.36 (34215) SS BOND : bond 0.00793 / 0.59 ( 39) SS BOND : angle 2.24274 / 1.32 ( 78) hydrogen bonds : bond 0.04945 / 3.20 ( 1016) hydrogen bonds : angle 6.21860 / 4.31 ( 2793) link_BETA1-4 : bond 0.00549 / 0.31 ( 14) link_BETA1-4 : angle 1.78029 / 1.11 ( 42) link_NAG-ASN : bond 0.00441 / 0.30 ( 47) link_NAG-ASN : angle 3.39190 / 2.29 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 36 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 224 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: C 474 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: C 900 MET cc_start: 0.9034 (mtp) cc_final: 0.8803 (mtp) outliers start: 28 outliers final: 16 residues processed: 64 average time/residue: 0.1502 time to fit residues: 16.6489 Evaluate side-chains 47 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 147 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 334 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.053472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.038711 restraints weight = 155856.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039391 restraints weight = 100033.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039647 restraints weight = 64853.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039915 restraints weight = 61954.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039931 restraints weight = 52957.324| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25252 Z= 0.184 Angle : 0.641 10.382 34476 Z= 0.327 Chirality : 0.045 0.217 4075 Planarity : 0.004 0.043 4341 Dihedral : 6.048 75.873 3267 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.62 % Rotamer: Outliers : 1.47 % Allowed : 5.87 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2993 helix: 1.44 (0.20), residues: 686 sheet: -0.09 (0.20), residues: 622 loop : -0.73 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.002 PHE C1089 TRP 0.017 0.001 TRP C 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (25152) covalent geometry : angle 0.61631 / 0.32 (34215) SS BOND : bond 0.00478 / 0.30 ( 39) SS BOND : angle 1.34522 / 0.78 ( 78) hydrogen bonds : bond 0.04420 / 2.89 ( 1016) hydrogen bonds : angle 5.74384 / 3.98 ( 2793) link_BETA1-4 : bond 0.00359 / 0.19 ( 14) link_BETA1-4 : angle 1.37312 / 0.90 ( 42) link_NAG-ASN : bond 0.00339 / 0.22 ( 47) link_NAG-ASN : angle 2.58893 / 1.69 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 32 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 SER cc_start: 0.5489 (OUTLIER) cc_final: 0.4416 (p) REVERT: C 474 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: C 900 MET cc_start: 0.9063 (mtp) cc_final: 0.8780 (mtp) outliers start: 39 outliers final: 27 residues processed: 71 average time/residue: 0.1570 time to fit residues: 19.1941 Evaluate side-chains 56 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 88 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.037868 restraints weight = 155462.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.038619 restraints weight = 96365.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039180 restraints weight = 61157.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039245 restraints weight = 58116.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.039275 restraints weight = 50048.052| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 25252 Z= 0.267 Angle : 0.675 11.942 34476 Z= 0.343 Chirality : 0.046 0.222 4075 Planarity : 0.004 0.039 4341 Dihedral : 6.022 77.695 3265 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 1.84 % Allowed : 7.07 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2993 helix: 1.27 (0.20), residues: 694 sheet: -0.14 (0.19), residues: 627 loop : -0.83 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1014 TYR 0.021 0.002 TYR C1067 PHE 0.020 0.002 PHE C1089 TRP 0.015 0.002 TRP C 104 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (25152) covalent geometry : angle 0.64941 / 0.34 (34215) SS BOND : bond 0.00496 / 0.29 ( 39) SS BOND : angle 1.91172 / 1.12 ( 78) hydrogen bonds : bond 0.04558 / 2.97 ( 1016) hydrogen bonds : angle 5.78555 / 4.01 ( 2793) link_BETA1-4 : bond 0.00324 / 0.18 ( 14) link_BETA1-4 : angle 1.43289 / 0.93 ( 42) link_NAG-ASN : bond 0.00431 / 0.26 ( 47) link_NAG-ASN : angle 2.55281 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 29 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: C 474 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6624 (mp10) outliers start: 49 outliers final: 31 residues processed: 78 average time/residue: 0.1616 time to fit residues: 21.4970 Evaluate side-chains 60 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 27 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.053072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038265 restraints weight = 154593.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039178 restraints weight = 94915.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.039544 restraints weight = 57921.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039698 restraints weight = 55768.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039721 restraints weight = 48249.272| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 25252 Z= 0.164 Angle : 0.591 9.514 34476 Z= 0.301 Chirality : 0.044 0.181 4075 Planarity : 0.004 0.103 4341 Dihedral : 5.722 77.702 3265 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Rotamer: Outliers : 1.92 % Allowed : 7.90 % Favored : 90.18 % 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: 2993 helix: 1.55 (0.20), residues: 693 sheet: -0.13 (0.19), residues: 638 loop : -0.76 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 214 TYR 0.019 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (25152) covalent geometry : angle 0.56804 / 0.30 (34215) SS BOND : bond 0.00465 / 0.32 ( 39) SS BOND : angle 1.63476 / 0.94 ( 78) hydrogen bonds : bond 0.04059 / 2.65 ( 1016) hydrogen bonds : angle 5.53329 / 3.82 ( 2793) link_BETA1-4 : bond 0.00326 / 0.18 ( 14) link_BETA1-4 : angle 1.24807 / 0.83 ( 42) link_NAG-ASN : bond 0.00274 / 0.18 ( 47) link_NAG-ASN : angle 2.26126 / 1.47 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 29 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 474 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7216 (tp40) REVERT: A 581 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8846 (p) REVERT: B 346 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: B 697 MET cc_start: 0.8486 (ttp) cc_final: 0.8260 (ttm) REVERT: C 474 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6567 (mp10) outliers start: 51 outliers final: 32 residues processed: 80 average time/residue: 0.1445 time to fit residues: 20.2051 Evaluate side-chains 63 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 26 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 114 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 121 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.053086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038342 restraints weight = 154272.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039150 restraints weight = 94182.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039666 restraints weight = 58684.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039759 restraints weight = 56573.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039796 restraints weight = 48173.455| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25252 Z= 0.156 Angle : 0.568 10.213 34476 Z= 0.288 Chirality : 0.043 0.178 4075 Planarity : 0.003 0.038 4341 Dihedral : 5.580 77.268 3265 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 8.65 % Favored : 89.62 % 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: -0.07 (0.15), residues: 2993 helix: 1.62 (0.20), residues: 694 sheet: -0.11 (0.19), residues: 639 loop : -0.73 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE B 456 TRP 0.011 0.001 TRP C 104 HIS 0.017 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (25152) covalent geometry : angle 0.54703 / 0.28 (34215) SS BOND : bond 0.00386 / 0.24 ( 39) SS BOND : angle 1.34997 / 0.77 ( 78) hydrogen bonds : bond 0.03888 / 2.53 ( 1016) hydrogen bonds : angle 5.41707 / 3.74 ( 2793) link_BETA1-4 : bond 0.00316 / 0.17 ( 14) link_BETA1-4 : angle 1.20938 / 0.81 ( 42) link_NAG-ASN : bond 0.00258 / 0.16 ( 47) link_NAG-ASN : angle 2.17051 / 1.41 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 27 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7303 (tp40) REVERT: A 581 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 346 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7660 (tpt170) REVERT: C 474 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6735 (mp10) outliers start: 46 outliers final: 35 residues processed: 73 average time/residue: 0.1492 time to fit residues: 18.9521 Evaluate side-chains 65 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 26 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 71 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 301 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 229 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.052627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038032 restraints weight = 156558.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.038552 restraints weight = 97433.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.038594 restraints weight = 67993.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038972 restraints weight = 66177.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038959 restraints weight = 61308.456| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25252 Z= 0.239 Angle : 0.614 9.922 34476 Z= 0.312 Chirality : 0.045 0.188 4075 Planarity : 0.004 0.037 4341 Dihedral : 5.652 78.136 3265 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 1.77 % Allowed : 8.84 % Favored : 89.39 % 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 (0.15), residues: 2993 helix: 1.48 (0.20), residues: 695 sheet: -0.21 (0.19), residues: 635 loop : -0.84 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.002 PHE C 392 TRP 0.011 0.001 TRP C 104 HIS 0.015 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (25152) covalent geometry : angle 0.59493 / 0.31 (34215) SS BOND : bond 0.00491 / 0.34 ( 39) SS BOND : angle 1.29884 / 0.74 ( 78) hydrogen bonds : bond 0.04146 / 2.70 ( 1016) hydrogen bonds : angle 5.52026 / 3.81 ( 2793) link_BETA1-4 : bond 0.00297 / 0.17 ( 14) link_BETA1-4 : angle 1.26598 / 0.83 ( 42) link_NAG-ASN : bond 0.00366 / 0.22 ( 47) link_NAG-ASN : angle 2.20380 / 1.43 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 27 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8779 (mt) REVERT: A 241 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8847 (pp) REVERT: B 346 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7602 (tpt170) REVERT: C 474 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6795 (mp10) outliers start: 47 outliers final: 38 residues processed: 74 average time/residue: 0.1493 time to fit residues: 19.5343 Evaluate side-chains 68 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 26 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 131 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.053548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038629 restraints weight = 153481.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039614 restraints weight = 83556.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040251 restraints weight = 57124.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.040673 restraints weight = 44993.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040919 restraints weight = 38741.417| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 25252 Z= 0.100 Angle : 0.525 11.715 34476 Z= 0.268 Chirality : 0.043 0.157 4075 Planarity : 0.003 0.037 4341 Dihedral : 5.328 76.817 3265 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.32 % Allowed : 9.52 % Favored : 89.16 % 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: 0.10 (0.15), residues: 2993 helix: 1.97 (0.20), residues: 683 sheet: 0.02 (0.20), residues: 642 loop : -0.72 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE C 392 TRP 0.010 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25152) covalent geometry : angle 0.50480 / 0.26 (34215) SS BOND : bond 0.00380 / 0.26 ( 39) SS BOND : angle 1.73473 / 1.03 ( 78) hydrogen bonds : bond 0.03500 / 2.28 ( 1016) hydrogen bonds : angle 5.22070 / 3.60 ( 2793) link_BETA1-4 : bond 0.00386 / 0.22 ( 14) link_BETA1-4 : angle 1.09876 / 0.74 ( 42) link_NAG-ASN : bond 0.00180 / 0.12 ( 47) link_NAG-ASN : angle 1.84783 / 1.19 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 28 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8713 (pp) REVERT: A 1050 MET cc_start: 0.7943 (mtm) cc_final: 0.7633 (mtp) REVERT: B 224 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: C 979 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8839 (t0) outliers start: 35 outliers final: 27 residues processed: 63 average time/residue: 0.1663 time to fit residues: 17.9740 Evaluate side-chains 56 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 26 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.052927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.038312 restraints weight = 155971.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038964 restraints weight = 96737.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039127 restraints weight = 64544.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039297 restraints weight = 66612.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039382 restraints weight = 56636.529| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25252 Z= 0.184 Angle : 0.578 12.031 34476 Z= 0.293 Chirality : 0.044 0.178 4075 Planarity : 0.003 0.056 4341 Dihedral : 5.459 76.556 3265 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 1.28 % Allowed : 9.63 % Favored : 89.09 % Cbeta Deviations : 0.00 % 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: -0.03 (0.15), residues: 2993 helix: 1.72 (0.20), residues: 695 sheet: -0.02 (0.19), residues: 650 loop : -0.77 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.018 0.001 TYR C1067 PHE 0.017 0.001 PHE C 392 TRP 0.009 0.001 TRP C 104 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (25152) covalent geometry : angle 0.55610 / 0.29 (34215) SS BOND : bond 0.00436 / 0.27 ( 39) SS BOND : angle 2.00665 / 1.15 ( 78) hydrogen bonds : bond 0.03842 / 2.51 ( 1016) hydrogen bonds : angle 5.32378 / 3.67 ( 2793) link_BETA1-4 : bond 0.00309 / 0.17 ( 14) link_BETA1-4 : angle 1.19054 / 0.79 ( 42) link_NAG-ASN : bond 0.00331 / 0.21 ( 47) link_NAG-ASN : angle 1.99011 / 1.28 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 26 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 902 MET cc_start: 0.9069 (tpt) cc_final: 0.8602 (tpt) REVERT: A 1050 MET cc_start: 0.7942 (mtm) cc_final: 0.7700 (mtp) outliers start: 34 outliers final: 30 residues processed: 60 average time/residue: 0.1477 time to fit residues: 15.3185 Evaluate side-chains 57 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 26 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 136 optimal weight: 0.0970 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 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 = 0.3490 r_free = 0.3490 target = 0.052826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038249 restraints weight = 156162.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038687 restraints weight = 103755.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.038894 restraints weight = 69287.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039100 restraints weight = 65973.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039173 restraints weight = 58567.801| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25252 Z= 0.195 Angle : 0.580 10.715 34476 Z= 0.295 Chirality : 0.044 0.218 4075 Planarity : 0.003 0.054 4341 Dihedral : 5.463 76.828 3265 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 1.20 % Allowed : 9.78 % Favored : 89.01 % 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: -0.11 (0.15), residues: 2993 helix: 1.64 (0.20), residues: 695 sheet: -0.04 (0.19), residues: 639 loop : -0.84 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.019 0.001 TYR C1067 PHE 0.017 0.001 PHE C 392 TRP 0.010 0.001 TRP C 104 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (25152) covalent geometry : angle 0.55970 / 0.29 (34215) SS BOND : bond 0.00437 / 0.28 ( 39) SS BOND : angle 1.83706 / 1.06 ( 78) hydrogen bonds : bond 0.03887 / 2.54 ( 1016) hydrogen bonds : angle 5.33656 / 3.68 ( 2793) link_BETA1-4 : bond 0.00322 / 0.18 ( 14) link_BETA1-4 : angle 1.15009 / 0.77 ( 42) link_NAG-ASN : bond 0.00313 / 0.20 ( 47) link_NAG-ASN : angle 1.96739 / 1.26 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 26 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8780 (pp) REVERT: A 902 MET cc_start: 0.9083 (tpt) cc_final: 0.8594 (tpt) REVERT: A 1050 MET cc_start: 0.7961 (mtm) cc_final: 0.7714 (mtp) outliers start: 32 outliers final: 30 residues processed: 58 average time/residue: 0.1578 time to fit residues: 15.7498 Evaluate side-chains 57 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 26 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 69 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.053204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038742 restraints weight = 156124.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039144 restraints weight = 102825.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039297 restraints weight = 69411.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039441 restraints weight = 65784.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039537 restraints weight = 59188.469| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25252 Z= 0.140 Angle : 0.544 9.400 34476 Z= 0.278 Chirality : 0.043 0.185 4075 Planarity : 0.003 0.052 4341 Dihedral : 5.325 76.623 3265 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 1.35 % Allowed : 9.63 % Favored : 89.01 % 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: -0.00 (0.15), residues: 2993 helix: 1.76 (0.20), residues: 696 sheet: -0.04 (0.19), residues: 649 loop : -0.75 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.019 0.001 TYR C1067 PHE 0.015 0.001 PHE C 392 TRP 0.010 0.001 TRP C 104 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (25152) covalent geometry : angle 0.52392 / 0.27 (34215) SS BOND : bond 0.00355 / 0.21 ( 39) SS BOND : angle 1.88308 / 1.05 ( 78) hydrogen bonds : bond 0.03644 / 2.39 ( 1016) hydrogen bonds : angle 5.22558 / 3.60 ( 2793) link_BETA1-4 : bond 0.00349 / 0.19 ( 14) link_BETA1-4 : angle 1.07800 / 0.73 ( 42) link_NAG-ASN : bond 0.00219 / 0.14 ( 47) link_NAG-ASN : angle 1.83758 / 1.17 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.99 seconds wall clock time: 57 minutes 42.43 seconds (3462.43 seconds total)