Starting phenix.real_space_refine on Sun Jul 5 00:30:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r13_14229/07_2026/7r13_14229.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 15498 2.51 5 N 3960 2.21 5 O 4740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 24303 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 Chain: "B" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 Chain: "C" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.56, per 1000 atoms: 0.23 Number of scatterers: 24303 At special positions: 0 Unit cell: (136.962, 136.962, 180.442, 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 4740 8.00 N 3960 7.00 C 15498 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 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=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 603 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 603 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C1134 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 24.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.746A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.310A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.881A pdb=" N SER A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.527A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.671A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (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: 3.508A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.621A pdb=" N ALA A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.209A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.747A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.310A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.882A pdb=" N SER B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.527A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.671A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 977 through 982 removed outlier: 3.622A pdb=" N ALA B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.210A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.747A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.311A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.881A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.527A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.672A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.622A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.210A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.070A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.049A 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: 11.395A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.593A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.629A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.857A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.935A 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: 5.572A 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 1122 removed outlier: 3.598A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.394A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.592A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.613A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.857A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.598A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 11.395A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.858A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.598A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7710 1.35 - 1.47: 6465 1.47 - 1.60: 10539 1.60 - 1.72: 0 1.72 - 1.85: 129 Bond restraints: 24843 Sorted by residual: bond pdb=" N CYS C 379 " pdb=" CA CYS C 379 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.58e+00 bond pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.57e+00 bond pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.37e+00 bond pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.94e+00 ... (remaining 24838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 32242 1.27 - 2.54: 1212 2.54 - 3.81: 293 3.81 - 5.08: 52 5.08 - 6.35: 8 Bond angle restraints: 33807 Sorted by residual: angle pdb=" CA ASN C 122 " pdb=" C ASN C 122 " pdb=" O ASN C 122 " ideal model delta sigma weight residual 121.50 117.97 3.53 1.25e+00 6.40e-01 7.97e+00 angle pdb=" CA ASN A 122 " pdb=" C ASN A 122 " pdb=" O ASN A 122 " ideal model delta sigma weight residual 121.50 117.99 3.51 1.25e+00 6.40e-01 7.90e+00 angle pdb=" CA ASN B 122 " pdb=" C ASN B 122 " pdb=" O ASN B 122 " ideal model delta sigma weight residual 121.50 118.01 3.49 1.25e+00 6.40e-01 7.81e+00 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 111.36 114.39 -3.03 1.09e+00 8.42e-01 7.74e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.09 -3.39 1.22e+00 6.72e-01 7.72e+00 ... (remaining 33802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 13162 17.01 - 34.02: 908 34.02 - 51.03: 201 51.03 - 68.04: 30 68.04 - 85.06: 36 Dihedral angle restraints: 14337 sinusoidal: 5598 harmonic: 8739 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.34 56.34 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.33 56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.32 56.32 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 14334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2769 0.040 - 0.080: 808 0.080 - 0.120: 385 0.120 - 0.160: 35 0.160 - 0.200: 8 Chirality restraints: 4005 Sorted by residual: chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA CYS B 379 " pdb=" N CYS B 379 " pdb=" C CYS B 379 " pdb=" CB CYS B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 4002 not shown) Planarity restraints: 4353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.013 2.00e-02 2.50e+03 1.21e-02 2.57e+00 pdb=" CG PHE B 906 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.013 2.00e-02 2.50e+03 1.20e-02 2.53e+00 pdb=" CG PHE A 906 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.013 2.00e-02 2.50e+03 1.20e-02 2.51e+00 pdb=" CG PHE C 906 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.000 2.00e-02 2.50e+03 ... (remaining 4350 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3836 2.77 - 3.30: 22121 3.30 - 3.83: 37741 3.83 - 4.37: 42046 4.37 - 4.90: 75058 Nonbonded interactions: 180802 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.234 3.040 ... (remaining 180797 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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' } 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.380 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24939 Z= 0.189 Angle : 0.605 6.346 34056 Z= 0.313 Chirality : 0.045 0.200 4005 Planarity : 0.003 0.035 4305 Dihedral : 12.788 85.055 8592 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2949 helix: 1.68 (0.22), residues: 621 sheet: 0.17 (0.19), residues: 684 loop : -1.43 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.015 0.001 TYR C 380 PHE 0.028 0.001 PHE B 906 TRP 0.026 0.002 TRP B 353 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (24843) covalent geometry : angle 0.59582 / 0.31 (33807) SS BOND : bond 0.01041 / 0.75 ( 39) SS BOND : angle 1.27273 / 0.95 ( 78) hydrogen bonds : bond 0.21293 / 14.26 ( 865) hydrogen bonds : angle 7.53484 / 5.09 ( 2334) link_BETA1-4 : bond 0.00300 / 0.18 ( 9) link_BETA1-4 : angle 0.89518 / 0.85 ( 27) link_NAG-ASN : bond 0.00186 / 0.12 ( 48) link_NAG-ASN : angle 1.44163 / 1.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8648 (p90) cc_final: 0.8197 (p90) REVERT: C 515 PHE cc_start: 0.8772 (p90) cc_final: 0.8075 (p90) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1622 time to fit residues: 78.4786 Evaluate side-chains 211 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 498 GLN A 804 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 498 GLN B 675 GLN B 804 GLN C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 498 GLN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110762 restraints weight = 38067.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109622 restraints weight = 42752.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111305 restraints weight = 44860.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111516 restraints weight = 29421.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113048 restraints weight = 26342.675| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24939 Z= 0.133 Angle : 0.568 6.648 34056 Z= 0.295 Chirality : 0.044 0.169 4005 Planarity : 0.004 0.038 4305 Dihedral : 4.099 20.381 3213 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.65 % Allowed : 5.87 % Favored : 93.49 % 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: -0.52 (0.15), residues: 2949 helix: 1.59 (0.22), residues: 630 sheet: 0.22 (0.19), residues: 738 loop : -1.49 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.018 0.001 TYR A 453 PHE 0.015 0.001 PHE B 32 TRP 0.015 0.002 TRP B 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24843) covalent geometry : angle 0.55697 / 0.29 (33807) SS BOND : bond 0.00564 / 0.40 ( 39) SS BOND : angle 1.22704 / 0.88 ( 78) hydrogen bonds : bond 0.05319 / 3.49 ( 865) hydrogen bonds : angle 5.65975 / 3.83 ( 2334) link_BETA1-4 : bond 0.00385 / 0.24 ( 9) link_BETA1-4 : angle 0.99180 / 0.94 ( 27) link_NAG-ASN : bond 0.00201 / 0.13 ( 48) link_NAG-ASN : angle 1.53239 / 1.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.903 Fit side-chains REVERT: A 368 LEU cc_start: 0.8874 (mp) cc_final: 0.8501 (mt) REVERT: A 781 VAL cc_start: 0.8653 (t) cc_final: 0.8448 (t) REVERT: B 102 ARG cc_start: 0.7492 (mmp-170) cc_final: 0.7194 (mmp-170) REVERT: B 675 GLN cc_start: 0.6841 (mt0) cc_final: 0.6613 (mt0) REVERT: C 102 ARG cc_start: 0.7468 (mmp-170) cc_final: 0.7219 (mmp-170) REVERT: C 515 PHE cc_start: 0.8770 (p90) cc_final: 0.7963 (p90) outliers start: 17 outliers final: 10 residues processed: 261 average time/residue: 0.1602 time to fit residues: 67.4713 Evaluate side-chains 222 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 615 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 231 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 241 optimal weight: 20.0000 chunk 120 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109374 restraints weight = 37865.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108012 restraints weight = 41816.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109336 restraints weight = 43704.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110427 restraints weight = 28214.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110868 restraints weight = 25604.150| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24939 Z= 0.135 Angle : 0.538 6.223 34056 Z= 0.279 Chirality : 0.044 0.188 4005 Planarity : 0.004 0.039 4305 Dihedral : 4.058 19.699 3213 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.41 % Allowed : 8.11 % Favored : 90.48 % 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: -0.48 (0.15), residues: 2949 helix: 1.60 (0.22), residues: 630 sheet: 0.26 (0.19), residues: 738 loop : -1.47 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.022 0.001 TYR B 453 PHE 0.026 0.001 PHE A 377 TRP 0.016 0.002 TRP B 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24843) covalent geometry : angle 0.52747 / 0.28 (33807) SS BOND : bond 0.00500 / 0.35 ( 39) SS BOND : angle 1.10092 / 0.76 ( 78) hydrogen bonds : bond 0.05136 / 3.37 ( 865) hydrogen bonds : angle 5.31489 / 3.59 ( 2334) link_BETA1-4 : bond 0.00304 / 0.19 ( 9) link_BETA1-4 : angle 0.95890 / 0.88 ( 27) link_NAG-ASN : bond 0.00196 / 0.12 ( 48) link_NAG-ASN : angle 1.51028 / 1.10 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7628 (mmp-170) cc_final: 0.7201 (mmp-170) REVERT: A 408 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7750 (tmm-80) REVERT: A 781 VAL cc_start: 0.8697 (t) cc_final: 0.8424 (t) REVERT: A 1029 MET cc_start: 0.9221 (tpp) cc_final: 0.8873 (ttm) REVERT: B 102 ARG cc_start: 0.7429 (mmp-170) cc_final: 0.7112 (mmp-170) REVERT: B 675 GLN cc_start: 0.6868 (mt0) cc_final: 0.6652 (mt0) REVERT: B 917 TYR cc_start: 0.8739 (m-80) cc_final: 0.7804 (m-80) REVERT: C 102 ARG cc_start: 0.7568 (mmp-170) cc_final: 0.7318 (mmp-170) REVERT: C 408 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7622 (tmm-80) REVERT: C 619 GLU cc_start: 0.7405 (mp0) cc_final: 0.7171 (mp0) outliers start: 37 outliers final: 30 residues processed: 255 average time/residue: 0.1424 time to fit residues: 59.5662 Evaluate side-chains 234 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 258 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105607 restraints weight = 37822.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104342 restraints weight = 41279.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105492 restraints weight = 38727.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106105 restraints weight = 28415.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106467 restraints weight = 25887.524| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24939 Z= 0.219 Angle : 0.596 6.268 34056 Z= 0.307 Chirality : 0.046 0.169 4005 Planarity : 0.004 0.039 4305 Dihedral : 4.273 21.130 3213 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.87 % Allowed : 9.52 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.58 (0.15), residues: 2949 helix: 1.55 (0.22), residues: 606 sheet: 0.16 (0.19), residues: 681 loop : -1.42 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.018 0.001 TYR B 904 PHE 0.023 0.002 PHE B 140 TRP 0.015 0.001 TRP B 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (24843) covalent geometry : angle 0.58405 / 0.30 (33807) SS BOND : bond 0.00709 / 0.48 ( 39) SS BOND : angle 1.33412 / 0.92 ( 78) hydrogen bonds : bond 0.05899 / 3.87 ( 865) hydrogen bonds : angle 5.32549 / 3.61 ( 2334) link_BETA1-4 : bond 0.00197 / 0.12 ( 9) link_BETA1-4 : angle 0.94153 / 0.87 ( 27) link_NAG-ASN : bond 0.00213 / 0.16 ( 48) link_NAG-ASN : angle 1.68907 / 1.25 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8222 (mp) cc_final: 0.7998 (tt) REVERT: A 1029 MET cc_start: 0.9198 (tpp) cc_final: 0.8932 (ttm) REVERT: B 102 ARG cc_start: 0.7599 (mmp-170) cc_final: 0.7146 (mmp-170) REVERT: B 374 PHE cc_start: 0.7934 (m-10) cc_final: 0.7731 (m-10) REVERT: C 102 ARG cc_start: 0.7911 (mmp-170) cc_final: 0.7645 (mmp-170) REVERT: C 408 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7692 (tmm-80) outliers start: 49 outliers final: 41 residues processed: 251 average time/residue: 0.1390 time to fit residues: 57.8580 Evaluate side-chains 236 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 59 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 299 optimal weight: 0.0970 chunk 141 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 293 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.3733 r_free = 0.3733 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107627 restraints weight = 37742.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106485 restraints weight = 39706.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107668 restraints weight = 42435.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108537 restraints weight = 27739.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108886 restraints weight = 25349.692| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24939 Z= 0.142 Angle : 0.546 7.825 34056 Z= 0.280 Chirality : 0.044 0.170 4005 Planarity : 0.003 0.038 4305 Dihedral : 4.174 19.770 3213 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.79 % Allowed : 11.47 % Favored : 86.74 % 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: -0.57 (0.15), residues: 2949 helix: 1.42 (0.22), residues: 633 sheet: 0.17 (0.19), residues: 714 loop : -1.43 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 408 TYR 0.026 0.001 TYR C 904 PHE 0.027 0.001 PHE B 140 TRP 0.022 0.002 TRP C 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (24843) covalent geometry : angle 0.53486 / 0.28 (33807) SS BOND : bond 0.00499 / 0.35 ( 39) SS BOND : angle 1.21222 / 0.85 ( 78) hydrogen bonds : bond 0.05175 / 3.39 ( 865) hydrogen bonds : angle 5.15081 / 3.49 ( 2334) link_BETA1-4 : bond 0.00282 / 0.18 ( 9) link_BETA1-4 : angle 0.92421 / 0.87 ( 27) link_NAG-ASN : bond 0.00198 / 0.13 ( 48) link_NAG-ASN : angle 1.52905 / 1.13 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.7264 (mmp-170) REVERT: A 353 TRP cc_start: 0.8042 (p-90) cc_final: 0.7395 (p-90) REVERT: A 781 VAL cc_start: 0.8724 (t) cc_final: 0.8449 (t) REVERT: A 1029 MET cc_start: 0.9185 (tpp) cc_final: 0.8901 (ttm) REVERT: B 102 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.7061 (mmp-170) REVERT: C 102 ARG cc_start: 0.7486 (mmp-170) cc_final: 0.7125 (mmp-170) REVERT: C 408 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7441 (tmm160) REVERT: C 409 GLN cc_start: 0.8071 (mt0) cc_final: 0.7834 (mt0) outliers start: 47 outliers final: 35 residues processed: 255 average time/residue: 0.1414 time to fit residues: 59.5047 Evaluate side-chains 238 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 212 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 265 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.3718 r_free = 0.3718 target = 0.143439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107595 restraints weight = 37922.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107146 restraints weight = 38056.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108154 restraints weight = 36092.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108819 restraints weight = 27411.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109033 restraints weight = 27016.254| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24939 Z= 0.170 Angle : 0.560 6.002 34056 Z= 0.288 Chirality : 0.044 0.168 4005 Planarity : 0.003 0.036 4305 Dihedral : 4.195 20.325 3213 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.10 % Allowed : 12.61 % Favored : 85.30 % 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: -0.61 (0.15), residues: 2949 helix: 1.35 (0.22), residues: 633 sheet: 0.15 (0.19), residues: 714 loop : -1.45 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.030 0.001 TYR C 904 PHE 0.027 0.001 PHE B 140 TRP 0.021 0.001 TRP C 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (24843) covalent geometry : angle 0.54856 / 0.29 (33807) SS BOND : bond 0.00557 / 0.39 ( 39) SS BOND : angle 1.28420 / 0.88 ( 78) hydrogen bonds : bond 0.05465 / 3.60 ( 865) hydrogen bonds : angle 5.13544 / 3.48 ( 2334) link_BETA1-4 : bond 0.00225 / 0.15 ( 9) link_BETA1-4 : angle 0.93422 / 0.87 ( 27) link_NAG-ASN : bond 0.00196 / 0.14 ( 48) link_NAG-ASN : angle 1.57987 / 1.17 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8086 (p-90) cc_final: 0.7478 (p-90) REVERT: A 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8785 (ttm) REVERT: B 102 ARG cc_start: 0.7535 (mmp-170) cc_final: 0.7127 (mmp-170) REVERT: B 1050 MET cc_start: 0.8725 (ptp) cc_final: 0.8484 (ptp) REVERT: C 102 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7182 (mmp-170) outliers start: 55 outliers final: 47 residues processed: 257 average time/residue: 0.1416 time to fit residues: 60.3300 Evaluate side-chains 252 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 0.0980 chunk 256 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 282 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS B 519 HIS C 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109114 restraints weight = 37713.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106834 restraints weight = 47286.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108428 restraints weight = 43945.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108998 restraints weight = 29596.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109362 restraints weight = 27342.692| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24939 Z= 0.121 Angle : 0.530 6.142 34056 Z= 0.272 Chirality : 0.043 0.169 4005 Planarity : 0.003 0.037 4305 Dihedral : 4.067 18.954 3213 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.02 % Allowed : 13.41 % Favored : 84.57 % 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: -0.41 (0.15), residues: 2949 helix: 1.92 (0.22), residues: 588 sheet: 0.19 (0.19), residues: 744 loop : -1.39 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.029 0.001 TYR C 904 PHE 0.029 0.001 PHE A 377 TRP 0.023 0.001 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (24843) covalent geometry : angle 0.51933 / 0.27 (33807) SS BOND : bond 0.00468 / 0.32 ( 39) SS BOND : angle 1.17559 / 0.82 ( 78) hydrogen bonds : bond 0.04859 / 3.20 ( 865) hydrogen bonds : angle 5.03449 / 3.40 ( 2334) link_BETA1-4 : bond 0.00311 / 0.19 ( 9) link_BETA1-4 : angle 0.92183 / 0.86 ( 27) link_NAG-ASN : bond 0.00200 / 0.13 ( 48) link_NAG-ASN : angle 1.46006 / 1.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8564 (m-80) cc_final: 0.8359 (m-10) REVERT: A 102 ARG cc_start: 0.7496 (mmp-170) cc_final: 0.7204 (mmp-170) REVERT: A 353 TRP cc_start: 0.8014 (p-90) cc_final: 0.7489 (p-90) REVERT: A 781 VAL cc_start: 0.8646 (t) cc_final: 0.8302 (t) REVERT: A 1029 MET cc_start: 0.9226 (tpp) cc_final: 0.8746 (ttm) REVERT: B 88 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: B 102 ARG cc_start: 0.7508 (mmp-170) cc_final: 0.7040 (mmp-170) REVERT: B 1050 MET cc_start: 0.8687 (ptp) cc_final: 0.8460 (ptp) REVERT: C 102 ARG cc_start: 0.7530 (mmp-170) cc_final: 0.7140 (mmp-170) REVERT: C 228 ASP cc_start: 0.8171 (p0) cc_final: 0.7921 (p0) REVERT: C 408 ARG cc_start: 0.8178 (tmm160) cc_final: 0.7415 (tmm160) REVERT: C 902 MET cc_start: 0.8774 (tpp) cc_final: 0.8571 (tpp) outliers start: 53 outliers final: 42 residues processed: 259 average time/residue: 0.1424 time to fit residues: 61.0013 Evaluate side-chains 249 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** C 422 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 = 0.3721 r_free = 0.3721 target = 0.143788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107249 restraints weight = 37764.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105913 restraints weight = 40571.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107328 restraints weight = 45403.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107529 restraints weight = 30111.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108204 restraints weight = 26823.446| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24939 Z= 0.153 Angle : 0.551 6.186 34056 Z= 0.283 Chirality : 0.044 0.168 4005 Planarity : 0.003 0.036 4305 Dihedral : 4.082 19.249 3213 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.13 % Allowed : 13.75 % Favored : 84.11 % 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: -0.43 (0.15), residues: 2949 helix: 1.88 (0.22), residues: 588 sheet: 0.22 (0.19), residues: 714 loop : -1.40 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.030 0.001 TYR C 904 PHE 0.028 0.001 PHE B 377 TRP 0.023 0.001 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (24843) covalent geometry : angle 0.54045 / 0.28 (33807) SS BOND : bond 0.00530 / 0.37 ( 39) SS BOND : angle 1.27314 / 0.88 ( 78) hydrogen bonds : bond 0.05185 / 3.41 ( 865) hydrogen bonds : angle 5.03181 / 3.40 ( 2334) link_BETA1-4 : bond 0.00215 / 0.14 ( 9) link_BETA1-4 : angle 0.90950 / 0.86 ( 27) link_NAG-ASN : bond 0.00188 / 0.13 ( 48) link_NAG-ASN : angle 1.52183 / 1.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8568 (m-80) cc_final: 0.8352 (m-10) REVERT: A 102 ARG cc_start: 0.7623 (mmp-170) cc_final: 0.7344 (mmp-170) REVERT: A 353 TRP cc_start: 0.8100 (p-90) cc_final: 0.7641 (p-90) REVERT: A 740 MET cc_start: 0.7964 (tpp) cc_final: 0.7669 (tpp) REVERT: A 781 VAL cc_start: 0.8772 (t) cc_final: 0.8447 (t) REVERT: A 1029 MET cc_start: 0.9232 (tpp) cc_final: 0.8760 (ttm) REVERT: B 88 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: B 102 ARG cc_start: 0.7518 (mmp-170) cc_final: 0.7052 (mmp-170) REVERT: B 342 PHE cc_start: 0.8006 (m-10) cc_final: 0.7788 (m-10) REVERT: B 1050 MET cc_start: 0.8701 (ptp) cc_final: 0.8483 (ptp) REVERT: C 102 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7083 (mmp-170) REVERT: C 228 ASP cc_start: 0.8187 (p0) cc_final: 0.7916 (p0) REVERT: C 408 ARG cc_start: 0.8210 (tmm160) cc_final: 0.7439 (tmm160) REVERT: C 902 MET cc_start: 0.8957 (tpp) cc_final: 0.8647 (tpp) outliers start: 56 outliers final: 48 residues processed: 261 average time/residue: 0.1456 time to fit residues: 62.9790 Evaluate side-chains 255 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 187 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 450 ASN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104320 restraints weight = 38089.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102809 restraints weight = 41398.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104243 restraints weight = 42474.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105093 restraints weight = 28381.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105495 restraints weight = 26256.329| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 24939 Z= 0.225 Angle : 0.614 7.149 34056 Z= 0.314 Chirality : 0.046 0.189 4005 Planarity : 0.003 0.037 4305 Dihedral : 4.301 20.504 3213 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.21 % Allowed : 13.90 % Favored : 83.89 % 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: -0.63 (0.15), residues: 2949 helix: 1.48 (0.22), residues: 606 sheet: 0.09 (0.19), residues: 711 loop : -1.44 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.034 0.002 TYR C 904 PHE 0.023 0.002 PHE B 140 TRP 0.020 0.001 TRP C 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (24843) covalent geometry : angle 0.60214 / 0.31 (33807) SS BOND : bond 0.00643 / 0.45 ( 39) SS BOND : angle 1.43015 / 0.98 ( 78) hydrogen bonds : bond 0.05985 / 3.93 ( 865) hydrogen bonds : angle 5.19554 / 3.53 ( 2334) link_BETA1-4 : bond 0.00171 / 0.11 ( 9) link_BETA1-4 : angle 0.93362 / 0.87 ( 27) link_NAG-ASN : bond 0.00209 / 0.16 ( 48) link_NAG-ASN : angle 1.68967 / 1.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8666 (m-80) cc_final: 0.8424 (m-10) REVERT: A 102 ARG cc_start: 0.7722 (mmp-170) cc_final: 0.7486 (mmp-170) REVERT: A 353 TRP cc_start: 0.8243 (p-90) cc_final: 0.7763 (p-90) REVERT: A 1029 MET cc_start: 0.9190 (tpp) cc_final: 0.8809 (ttm) REVERT: B 102 ARG cc_start: 0.7739 (mmp-170) cc_final: 0.7362 (mmp-170) REVERT: B 619 GLU cc_start: 0.7729 (mp0) cc_final: 0.6860 (mp0) REVERT: B 1050 MET cc_start: 0.8734 (ptp) cc_final: 0.8499 (ptp) REVERT: C 102 ARG cc_start: 0.7551 (mmp-170) cc_final: 0.7121 (mmp-170) outliers start: 58 outliers final: 49 residues processed: 256 average time/residue: 0.1448 time to fit residues: 60.9142 Evaluate side-chains 252 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105886 restraints weight = 37771.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104980 restraints weight = 39268.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106162 restraints weight = 45488.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106595 restraints weight = 29411.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107784 restraints weight = 26552.009| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24939 Z= 0.163 Angle : 0.583 8.756 34056 Z= 0.298 Chirality : 0.045 0.172 4005 Planarity : 0.003 0.039 4305 Dihedral : 4.231 20.376 3213 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 14.40 % Favored : 83.70 % 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: -0.57 (0.15), residues: 2949 helix: 1.58 (0.22), residues: 606 sheet: 0.05 (0.19), residues: 744 loop : -1.41 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.038 0.001 TYR C 904 PHE 0.034 0.001 PHE B 377 TRP 0.023 0.001 TRP C 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (24843) covalent geometry : angle 0.57101 / 0.30 (33807) SS BOND : bond 0.00515 / 0.36 ( 39) SS BOND : angle 1.34190 / 0.93 ( 78) hydrogen bonds : bond 0.05510 / 3.62 ( 865) hydrogen bonds : angle 5.11531 / 3.47 ( 2334) link_BETA1-4 : bond 0.00220 / 0.14 ( 9) link_BETA1-4 : angle 0.92197 / 0.87 ( 27) link_NAG-ASN : bond 0.00194 / 0.13 ( 48) link_NAG-ASN : angle 1.60200 / 1.20 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7715 (mmp-170) cc_final: 0.7505 (mmp-170) REVERT: A 353 TRP cc_start: 0.8241 (p-90) cc_final: 0.7747 (p-90) REVERT: A 1029 MET cc_start: 0.9207 (tpp) cc_final: 0.8821 (ttm) REVERT: B 102 ARG cc_start: 0.7646 (mmp-170) cc_final: 0.7265 (mmp-170) REVERT: B 1050 MET cc_start: 0.8723 (ptp) cc_final: 0.8497 (ptp) REVERT: C 102 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7087 (mmp-170) outliers start: 50 outliers final: 47 residues processed: 253 average time/residue: 0.1523 time to fit residues: 63.6869 Evaluate side-chains 256 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 114 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 142 optimal weight: 0.0980 overall best weight: 0.8224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 422 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 = 0.3716 r_free = 0.3716 target = 0.143212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106038 restraints weight = 37931.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104981 restraints weight = 41611.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106478 restraints weight = 47438.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106764 restraints weight = 29186.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108428 restraints weight = 25808.039| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24939 Z= 0.149 Angle : 0.574 9.258 34056 Z= 0.293 Chirality : 0.044 0.172 4005 Planarity : 0.003 0.038 4305 Dihedral : 4.176 19.964 3213 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 14.48 % Favored : 83.62 % 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: -0.53 (0.15), residues: 2949 helix: 1.65 (0.22), residues: 606 sheet: 0.07 (0.19), residues: 744 loop : -1.41 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.036 0.001 TYR C 904 PHE 0.022 0.001 PHE B 140 TRP 0.022 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (24843) covalent geometry : angle 0.56249 / 0.29 (33807) SS BOND : bond 0.00483 / 0.34 ( 39) SS BOND : angle 1.29056 / 0.89 ( 78) hydrogen bonds : bond 0.05310 / 3.49 ( 865) hydrogen bonds : angle 5.05934 / 3.43 ( 2334) link_BETA1-4 : bond 0.00252 / 0.16 ( 9) link_BETA1-4 : angle 0.91446 / 0.86 ( 27) link_NAG-ASN : bond 0.00190 / 0.13 ( 48) link_NAG-ASN : angle 1.56638 / 1.17 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.05 seconds wall clock time: 60 minutes 46.86 seconds (3646.86 seconds total)