Starting phenix.real_space_refine on Sun Jul 5 18:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5h_24190/07_2026/7n5h_24190.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 123 5.16 5 C 18892 2.51 5 N 4864 2.21 5 O 5812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29691 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7894 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1011, 7894 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 51, 'TRANS': 959} Chain breaks: 7 Chain: "B" Number of atoms: 7911 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1013, 7911 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 51, 'TRANS': 961} Chain breaks: 7 Chain: "C" Number of atoms: 7894 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1010, 7894 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 7 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "F" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} 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: "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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.84, per 1000 atoms: 0.20 Number of scatterers: 29691 At special positions: 0 Unit cell: (153.01, 140.17, 195.81, 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 123 16.00 O 5812 8.00 N 4864 7.00 C 18892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.22 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B 282 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 709 " " NAG D 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B 331 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C 331 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6962 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 67 sheets defined 22.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.825A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.927A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.403A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.804A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.542A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.527A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.652A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.721A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.616A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.765A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.672A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.512A 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 976 through 984 removed outlier: 3.530A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.626A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.208A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.512A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.846A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.344A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.582A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.644A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.634A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.670A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.765A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.883A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.672A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.664A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.897A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.115A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.815A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.343A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.581A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.576A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.562A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.534A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.560A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.629A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.767A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.632A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.533A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.293A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.146A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.656A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.656A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.656A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.590A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.065A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.712A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.436A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 13.574A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.723A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.769A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.451A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.554A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.872A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.544A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.544A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.810A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.386A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.572A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.053A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.931A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.749A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.596A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.724A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.295A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.295A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.698A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.463A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.187A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.533A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.578A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.395A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.781A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.850A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.615A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.724A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.109A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.537A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.537A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.513A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N VAL L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.791A pdb=" N SER L 65 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.494A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.494A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 89 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 89 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.514A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N GLN F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N SER F 67 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL F 28 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 11.792A pdb=" N SER F 65 " --> pdb=" O VAL F 28 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.494A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.494A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AG9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 89 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.538A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 89 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.513A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR K 69 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N GLN K 27 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N SER K 67 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N VAL K 28 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 11.791A pdb=" N SER K 65 " --> pdb=" O VAL K 28 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.495A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.495A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2958 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: 7.66 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4811 1.29 - 1.43: 8285 1.43 - 1.57: 17114 1.57 - 1.70: 1 1.70 - 1.84: 153 Bond restraints: 30364 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" O CYS B 336 " ideal model delta sigma weight residual 1.235 1.154 0.081 1.28e-02 6.10e+03 4.04e+01 bond pdb=" C GLN C 409 " pdb=" N ILE C 410 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.36e-02 5.41e+03 2.54e+01 bond pdb=" C VAL B 407 " pdb=" N ARG B 408 " ideal model delta sigma weight residual 1.335 1.396 -0.060 1.32e-02 5.74e+03 2.09e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.52e+01 bond pdb=" CA SER E 31 " pdb=" CB SER E 31 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.60e-02 3.91e+03 1.50e+01 ... (remaining 30359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 37533 2.08 - 4.15: 3415 4.15 - 6.23: 305 6.23 - 8.31: 40 8.31 - 10.39: 24 Bond angle restraints: 41317 Sorted by residual: angle pdb=" C ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta sigma weight residual 116.54 107.11 9.43 1.15e+00 7.56e-01 6.72e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 119.03 -8.33 1.22e+00 6.72e-01 4.66e+01 angle pdb=" C GLU B 406 " pdb=" N VAL B 407 " pdb=" CA VAL B 407 " ideal model delta sigma weight residual 120.46 111.95 8.51 1.37e+00 5.33e-01 3.86e+01 angle pdb=" C GLU A 406 " pdb=" N VAL A 407 " pdb=" CA VAL A 407 " ideal model delta sigma weight residual 120.46 111.99 8.47 1.37e+00 5.33e-01 3.83e+01 angle pdb=" N THR L 56 " pdb=" CA THR L 56 " pdb=" C THR L 56 " ideal model delta sigma weight residual 111.96 103.34 8.62 1.41e+00 5.03e-01 3.74e+01 ... (remaining 41312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16261 17.86 - 35.72: 1183 35.72 - 53.58: 206 53.58 - 71.44: 48 71.44 - 89.30: 25 Dihedral angle restraints: 17723 sinusoidal: 6863 harmonic: 10860 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 0.15 -86.15 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 172.65 -79.65 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 169.66 -76.66 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 17720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4052 0.108 - 0.215: 627 0.215 - 0.323: 96 0.323 - 0.430: 7 0.430 - 0.538: 1 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CA TYR A 369 " pdb=" N TYR A 369 " pdb=" C TYR A 369 " pdb=" CB TYR A 369 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C2 NAG S 1 " pdb=" C1 NAG S 1 " pdb=" C3 NAG S 1 " pdb=" N2 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 4780 not shown) Planarity restraints: 5308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 458 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.67e+01 pdb=" C LYS B 458 " 0.089 2.00e-02 2.50e+03 pdb=" O LYS B 458 " -0.033 2.00e-02 2.50e+03 pdb=" N ASER B 459 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 458 " 0.025 2.00e-02 2.50e+03 5.15e-02 2.66e+01 pdb=" C LYS A 458 " -0.089 2.00e-02 2.50e+03 pdb=" O LYS A 458 " 0.033 2.00e-02 2.50e+03 pdb=" N ASER A 459 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 458 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C LYS C 458 " -0.089 2.00e-02 2.50e+03 pdb=" O LYS C 458 " 0.033 2.00e-02 2.50e+03 pdb=" N ASER C 459 " 0.031 2.00e-02 2.50e+03 ... (remaining 5305 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6724 2.79 - 3.32: 25183 3.32 - 3.85: 47969 3.85 - 4.37: 56097 4.37 - 4.90: 96090 Nonbonded interactions: 232063 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.267 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.282 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.285 3.040 nonbonded pdb=" O THR A 430 " pdb=" OG1 THR A 430 " model vdw 2.303 3.040 nonbonded pdb=" O THR C 430 " pdb=" OG1 THR C 430 " model vdw 2.303 3.040 ... (remaining 232058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 172 or resid 187 through 262 or resid 265 throu \ gh 811 or resid 813 through 1302)) selection = (chain 'B' and (resid 24 through 67 or resid 79 through 262 or resid 265 through \ 811 or resid 813 through 1302)) selection = (chain 'C' and (resid 24 through 67 or resid 79 through 143 or resid 157 through \ 172 or resid 187 through 1302)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.009 0.190 30450 Z= 0.602 Angle : 1.194 11.881 41530 Z= 0.814 Chirality : 0.080 0.538 4783 Planarity : 0.006 0.084 5283 Dihedral : 12.692 89.302 10626 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.12), residues: 3679 helix: -2.93 (0.12), residues: 621 sheet: 0.21 (0.17), residues: 834 loop : -1.13 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.029 0.002 TYR B 369 PHE 0.030 0.002 PHE A 86 TRP 0.019 0.002 TRP E 103 HIS 0.020 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.60 (30364) covalent geometry : angle 1.18708 / 0.81 (41317) SS BOND : bond 0.02873 / 2.17 ( 45) SS BOND : angle 1.64377 / 1.32 ( 90) hydrogen bonds : bond 0.25908 / 16.85 ( 1051) hydrogen bonds : angle 9.83780 / 6.69 ( 2958) link_BETA1-4 : bond 0.00722 / 0.50 ( 16) link_BETA1-4 : angle 2.10438 / 1.28 ( 48) link_NAG-ASN : bond 0.00321 / 0.33 ( 25) link_NAG-ASN : angle 2.55237 / 1.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 294 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 751 ASN cc_start: 0.8810 (m-40) cc_final: 0.8396 (m110) REVERT: H 23 THR cc_start: 0.6630 (m) cc_final: 0.6400 (p) outliers start: 6 outliers final: 1 residues processed: 299 average time/residue: 0.1856 time to fit residues: 87.8767 Evaluate side-chains 131 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 414 GLN A 422 ASN A 450 ASN A 498 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 448 ASN B 450 ASN B 498 GLN B 580 GLN C 334 ASN C 414 GLN C 422 ASN C 448 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1135 ASN L 6 GLN F 6 GLN F 37 GLN K 6 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.093211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.058536 restraints weight = 130819.516| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.08 r_work: 0.3144 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30450 Z= 0.169 Angle : 0.599 9.918 41530 Z= 0.314 Chirality : 0.043 0.275 4783 Planarity : 0.004 0.063 5283 Dihedral : 3.781 24.938 4029 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.74 % Allowed : 8.79 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.40 (0.13), residues: 3679 helix: 0.16 (0.19), residues: 658 sheet: 0.48 (0.16), residues: 959 loop : -0.75 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 18 TYR 0.023 0.001 TYR A 369 PHE 0.025 0.001 PHE A 338 TRP 0.015 0.002 TRP J 35A HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (30364) covalent geometry : angle 0.59152 / 0.31 (41317) SS BOND : bond 0.00316 / 0.24 ( 45) SS BOND : angle 0.96701 / 0.85 ( 90) hydrogen bonds : bond 0.04878 / 3.12 ( 1051) hydrogen bonds : angle 6.37971 / 4.39 ( 2958) link_BETA1-4 : bond 0.00281 / 0.18 ( 16) link_BETA1-4 : angle 1.31322 / 1.02 ( 48) link_NAG-ASN : bond 0.00275 / 0.17 ( 25) link_NAG-ASN : angle 1.89981 / 1.35 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 565 PHE cc_start: 0.7503 (m-10) cc_final: 0.7264 (m-80) REVERT: C 338 PHE cc_start: 0.7911 (m-10) cc_final: 0.7673 (m-10) REVERT: C 505 TYR cc_start: 0.9284 (m-10) cc_final: 0.8986 (t80) REVERT: C 731 MET cc_start: 0.7964 (ttt) cc_final: 0.7723 (ttt) REVERT: L 17 GLU cc_start: 0.4170 (tm-30) cc_final: 0.3591 (tt0) REVERT: E 87 THR cc_start: -0.0338 (OUTLIER) cc_final: -0.1137 (t) REVERT: E 108 MET cc_start: 0.7781 (tpt) cc_final: 0.6638 (pmm) REVERT: F 37 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.5492 (tp40) outliers start: 24 outliers final: 10 residues processed: 159 average time/residue: 0.2086 time to fit residues: 51.8001 Evaluate side-chains 118 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 119 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 276 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 414 GLN B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 913 GLN C 448 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.089107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053614 restraints weight = 124684.231| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.10 r_work: 0.2995 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 30450 Z= 0.304 Angle : 0.665 9.650 41530 Z= 0.343 Chirality : 0.046 0.278 4783 Planarity : 0.004 0.062 5283 Dihedral : 4.146 23.673 4029 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.08 % Allowed : 10.64 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.05 (0.13), residues: 3679 helix: 1.08 (0.20), residues: 654 sheet: 0.38 (0.16), residues: 968 loop : -0.57 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.035 0.002 TYR E 50 PHE 0.025 0.002 PHE A 906 TRP 0.023 0.002 TRP J 35A HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.30 (30364) covalent geometry : angle 0.65468 / 0.34 (41317) SS BOND : bond 0.00389 / 0.27 ( 45) SS BOND : angle 1.03971 / 0.96 ( 90) hydrogen bonds : bond 0.04500 / 2.90 ( 1051) hydrogen bonds : angle 5.94532 / 4.12 ( 2958) link_BETA1-4 : bond 0.00308 / 0.27 ( 16) link_BETA1-4 : angle 1.63424 / 1.63 ( 48) link_NAG-ASN : bond 0.00751 / 0.59 ( 25) link_NAG-ASN : angle 2.41615 / 1.77 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8320 (tmm) cc_final: 0.7825 (tmm) REVERT: B 342 PHE cc_start: 0.8299 (m-10) cc_final: 0.8053 (m-80) REVERT: B 565 PHE cc_start: 0.7842 (m-10) cc_final: 0.7517 (m-10) REVERT: B 869 MET cc_start: 0.9492 (mtm) cc_final: 0.9205 (mtm) REVERT: B 1050 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8627 (ptp) REVERT: C 338 PHE cc_start: 0.7923 (m-10) cc_final: 0.7514 (m-10) REVERT: C 505 TYR cc_start: 0.9328 (m-10) cc_final: 0.9001 (t80) REVERT: C 731 MET cc_start: 0.8480 (ttt) cc_final: 0.8128 (ttt) REVERT: C 869 MET cc_start: 0.9455 (mtm) cc_final: 0.9060 (ttm) REVERT: C 1050 MET cc_start: 0.9136 (ptp) cc_final: 0.8886 (ptp) REVERT: H 81 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8830 (mtmm) REVERT: L 17 GLU cc_start: 0.5054 (tm-30) cc_final: 0.4642 (tt0) REVERT: E 77 GLN cc_start: 0.7932 (pp30) cc_final: 0.7419 (pp30) REVERT: E 87 THR cc_start: -0.0697 (OUTLIER) cc_final: -0.1674 (t) REVERT: E 108 MET cc_start: 0.7943 (tpt) cc_final: 0.6931 (pmm) REVERT: F 33 LEU cc_start: 0.3208 (OUTLIER) cc_final: 0.2902 (tm) REVERT: J 43 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7406 (tmtt) REVERT: J 108 MET cc_start: 0.5272 (tpt) cc_final: 0.5021 (mmm) outliers start: 35 outliers final: 11 residues processed: 140 average time/residue: 0.1918 time to fit residues: 44.6423 Evaluate side-chains 102 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 154 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 367 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 356 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 357 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.090496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055639 restraints weight = 128187.587| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.04 r_work: 0.3077 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30450 Z= 0.124 Angle : 0.515 9.549 41530 Z= 0.265 Chirality : 0.043 0.253 4783 Planarity : 0.003 0.058 5283 Dihedral : 3.831 23.678 4029 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.98 % Allowed : 11.32 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3679 helix: 1.53 (0.20), residues: 654 sheet: 0.60 (0.16), residues: 945 loop : -0.47 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.021 0.001 TYR B 904 PHE 0.016 0.001 PHE F 62 TRP 0.030 0.001 TRP J 35A HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (30364) covalent geometry : angle 0.50935 / 0.26 (41317) SS BOND : bond 0.00258 / 0.17 ( 45) SS BOND : angle 0.66998 / 0.65 ( 90) hydrogen bonds : bond 0.03492 / 2.23 ( 1051) hydrogen bonds : angle 5.45379 / 3.78 ( 2958) link_BETA1-4 : bond 0.00313 / 0.23 ( 16) link_BETA1-4 : angle 1.17518 / 0.90 ( 48) link_NAG-ASN : bond 0.00176 / 0.11 ( 25) link_NAG-ASN : angle 1.61918 / 1.14 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8410 (tmm) cc_final: 0.7726 (tmm) REVERT: B 231 ILE cc_start: 0.9066 (pt) cc_final: 0.8844 (mm) REVERT: B 565 PHE cc_start: 0.7481 (m-10) cc_final: 0.7045 (m-10) REVERT: B 770 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9145 (tt) REVERT: B 869 MET cc_start: 0.9475 (mtm) cc_final: 0.9068 (mtm) REVERT: C 505 TYR cc_start: 0.9353 (m-10) cc_final: 0.9010 (t80) REVERT: C 731 MET cc_start: 0.8234 (ttt) cc_final: 0.7867 (ttt) REVERT: C 869 MET cc_start: 0.9401 (mtm) cc_final: 0.8940 (ttm) REVERT: C 900 MET cc_start: 0.9271 (ttm) cc_final: 0.9066 (mtt) REVERT: H 3 GLN cc_start: 0.9423 (mm110) cc_final: 0.9158 (tp40) REVERT: H 81 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8839 (mtmm) REVERT: L 17 GLU cc_start: 0.5219 (tm-30) cc_final: 0.4880 (tt0) REVERT: L 96 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: L 104 VAL cc_start: 0.4926 (OUTLIER) cc_final: 0.4706 (p) REVERT: E 51 MET cc_start: 0.4543 (ppp) cc_final: 0.4175 (pmm) REVERT: E 77 GLN cc_start: 0.8012 (pp30) cc_final: 0.7560 (pp30) REVERT: E 87 THR cc_start: -0.0826 (OUTLIER) cc_final: -0.1777 (t) REVERT: E 108 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6986 (pmm) REVERT: F 33 LEU cc_start: 0.3403 (OUTLIER) cc_final: 0.3126 (tm) REVERT: J 43 LYS cc_start: 0.7485 (mmmt) cc_final: 0.7248 (tmtt) REVERT: J 108 MET cc_start: 0.5149 (tpt) cc_final: 0.4682 (mmm) outliers start: 32 outliers final: 10 residues processed: 124 average time/residue: 0.2149 time to fit residues: 43.3959 Evaluate side-chains 99 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 25 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 321 optimal weight: 40.0000 chunk 274 optimal weight: 0.0050 chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 160 optimal weight: 0.0050 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 0.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 563 GLN B 965 GLN C 762 GLN L 42 GLN E 3 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.090444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055717 restraints weight = 127806.472| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.97 r_work: 0.3079 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30450 Z= 0.111 Angle : 0.499 9.537 41530 Z= 0.256 Chirality : 0.042 0.256 4783 Planarity : 0.003 0.069 5283 Dihedral : 3.676 20.626 4029 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.14 % Allowed : 12.15 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.14), residues: 3679 helix: 1.78 (0.21), residues: 652 sheet: 0.68 (0.16), residues: 952 loop : -0.39 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 61 TYR 0.031 0.001 TYR L 49 PHE 0.018 0.001 PHE B 338 TRP 0.036 0.001 TRP J 35A HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (30364) covalent geometry : angle 0.49166 / 0.25 (41317) SS BOND : bond 0.00221 / 0.15 ( 45) SS BOND : angle 0.96732 / 0.75 ( 90) hydrogen bonds : bond 0.03266 / 2.10 ( 1051) hydrogen bonds : angle 5.18576 / 3.60 ( 2958) link_BETA1-4 : bond 0.00241 / 0.19 ( 16) link_BETA1-4 : angle 1.25792 / 1.09 ( 48) link_NAG-ASN : bond 0.00156 / 0.12 ( 25) link_NAG-ASN : angle 1.60430 / 1.14 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 770 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9132 (tt) REVERT: B 1019 ARG cc_start: 0.9174 (tpt170) cc_final: 0.8947 (tpt170) REVERT: C 505 TYR cc_start: 0.9346 (m-10) cc_final: 0.8995 (t80) REVERT: C 731 MET cc_start: 0.8201 (ttt) cc_final: 0.7856 (ttt) REVERT: C 869 MET cc_start: 0.9429 (mtm) cc_final: 0.9028 (ttm) REVERT: H 81 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8821 (mtmm) REVERT: L 17 GLU cc_start: 0.5374 (tm-30) cc_final: 0.5113 (tt0) REVERT: L 96 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: L 104 VAL cc_start: 0.5031 (OUTLIER) cc_final: 0.4789 (p) REVERT: E 51 MET cc_start: 0.4861 (ppp) cc_final: 0.4560 (pmm) REVERT: E 77 GLN cc_start: 0.8103 (pp30) cc_final: 0.7668 (pp30) REVERT: E 87 THR cc_start: -0.0869 (OUTLIER) cc_final: -0.1831 (t) REVERT: E 108 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6986 (pmm) REVERT: F 33 LEU cc_start: 0.3176 (OUTLIER) cc_final: 0.2830 (tm) REVERT: J 35 TRP cc_start: 0.7817 (m-90) cc_final: 0.5783 (t-100) REVERT: J 108 MET cc_start: 0.5177 (tpt) cc_final: 0.4892 (mmm) REVERT: K 45 ARG cc_start: 0.8285 (mmm160) cc_final: 0.8068 (mmm160) outliers start: 37 outliers final: 13 residues processed: 125 average time/residue: 0.2099 time to fit residues: 42.5699 Evaluate side-chains 99 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 92 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 31 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 160 optimal weight: 0.0000 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 115 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.090022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055595 restraints weight = 125364.291| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.01 r_work: 0.3076 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30450 Z= 0.107 Angle : 0.483 9.584 41530 Z= 0.248 Chirality : 0.041 0.245 4783 Planarity : 0.003 0.054 5283 Dihedral : 3.602 18.308 4028 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.17 % Allowed : 12.12 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.14), residues: 3679 helix: 1.89 (0.21), residues: 656 sheet: 0.79 (0.16), residues: 942 loop : -0.36 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.025 0.001 TYR L 49 PHE 0.034 0.001 PHE B 342 TRP 0.023 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (30364) covalent geometry : angle 0.47737 / 0.25 (41317) SS BOND : bond 0.00214 / 0.14 ( 45) SS BOND : angle 0.73474 / 0.61 ( 90) hydrogen bonds : bond 0.03097 / 1.97 ( 1051) hydrogen bonds : angle 5.02334 / 3.50 ( 2958) link_BETA1-4 : bond 0.00281 / 0.22 ( 16) link_BETA1-4 : angle 1.18163 / 0.96 ( 48) link_NAG-ASN : bond 0.00108 / 0.07 ( 25) link_NAG-ASN : angle 1.49647 / 1.05 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: A 697 MET cc_start: 0.8378 (tmm) cc_final: 0.7877 (tmm) REVERT: B 770 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9115 (tt) REVERT: B 1019 ARG cc_start: 0.9174 (tpt170) cc_final: 0.8912 (tpt170) REVERT: C 731 MET cc_start: 0.8214 (ttt) cc_final: 0.7871 (ttt) REVERT: C 869 MET cc_start: 0.9411 (mtm) cc_final: 0.9001 (ttm) REVERT: H 3 GLN cc_start: 0.9414 (mm110) cc_final: 0.9158 (tp40) REVERT: H 81 LYS cc_start: 0.9232 (mmtm) cc_final: 0.8892 (mtmm) REVERT: L 17 GLU cc_start: 0.5543 (tm-30) cc_final: 0.5338 (tt0) REVERT: L 96 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: L 104 VAL cc_start: 0.5116 (OUTLIER) cc_final: 0.4858 (p) REVERT: E 51 MET cc_start: 0.5110 (OUTLIER) cc_final: 0.4837 (pmm) REVERT: E 77 GLN cc_start: 0.8172 (pp30) cc_final: 0.7771 (pp30) REVERT: E 87 THR cc_start: -0.1168 (OUTLIER) cc_final: -0.1989 (t) REVERT: E 108 MET cc_start: 0.7967 (tpt) cc_final: 0.7074 (pmm) REVERT: F 32 TYR cc_start: 0.8617 (m-80) cc_final: 0.8286 (m-80) REVERT: F 33 LEU cc_start: 0.2394 (OUTLIER) cc_final: 0.2127 (tm) REVERT: J 43 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7635 (tmtt) REVERT: J 46 GLU cc_start: 0.7564 (tp30) cc_final: 0.7103 (tp30) REVERT: J 108 MET cc_start: 0.5053 (tpt) cc_final: 0.4771 (mmm) REVERT: K 45 ARG cc_start: 0.8279 (mmm160) cc_final: 0.8058 (mmm160) REVERT: K 104 VAL cc_start: 0.0307 (OUTLIER) cc_final: -0.0007 (t) outliers start: 38 outliers final: 16 residues processed: 126 average time/residue: 0.2008 time to fit residues: 41.5730 Evaluate side-chains 106 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 351 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 320 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 935 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.089347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054461 restraints weight = 125212.828| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.07 r_work: 0.3048 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30450 Z= 0.155 Angle : 0.509 9.482 41530 Z= 0.260 Chirality : 0.042 0.256 4783 Planarity : 0.003 0.053 5283 Dihedral : 3.662 17.302 4028 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.23 % Allowed : 12.45 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.56 (0.14), residues: 3679 helix: 1.94 (0.21), residues: 656 sheet: 0.77 (0.16), residues: 949 loop : -0.31 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.021 0.001 TYR C 369 PHE 0.024 0.001 PHE B 342 TRP 0.042 0.001 TRP J 35A HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (30364) covalent geometry : angle 0.50240 / 0.26 (41317) SS BOND : bond 0.00246 / 0.17 ( 45) SS BOND : angle 0.75414 / 0.65 ( 90) hydrogen bonds : bond 0.03201 / 2.06 ( 1051) hydrogen bonds : angle 5.03884 / 3.52 ( 2958) link_BETA1-4 : bond 0.00158 / 0.14 ( 16) link_BETA1-4 : angle 1.27983 / 1.19 ( 48) link_NAG-ASN : bond 0.00268 / 0.21 ( 25) link_NAG-ASN : angle 1.68075 / 1.21 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: A 697 MET cc_start: 0.8418 (tmm) cc_final: 0.7535 (tmm) REVERT: B 770 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9128 (tt) REVERT: B 1002 GLN cc_start: 0.9220 (tp40) cc_final: 0.8863 (tp40) REVERT: B 1019 ARG cc_start: 0.9210 (tpt170) cc_final: 0.8985 (tpt170) REVERT: C 130 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6538 (t) REVERT: C 731 MET cc_start: 0.8277 (ttt) cc_final: 0.7901 (ttt) REVERT: C 869 MET cc_start: 0.9433 (mtm) cc_final: 0.8986 (ttm) REVERT: H 3 GLN cc_start: 0.9417 (mm110) cc_final: 0.9125 (tm-30) REVERT: H 81 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8808 (mtmm) REVERT: L 17 GLU cc_start: 0.5494 (tm-30) cc_final: 0.4897 (pt0) REVERT: L 60 ASP cc_start: 0.8359 (m-30) cc_final: 0.7768 (m-30) REVERT: L 61 ARG cc_start: 0.8438 (mmp80) cc_final: 0.8195 (ptt180) REVERT: L 96 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: L 104 VAL cc_start: 0.4989 (OUTLIER) cc_final: 0.4751 (p) REVERT: E 51 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4644 (pmm) REVERT: E 77 GLN cc_start: 0.8153 (pp30) cc_final: 0.7703 (pp30) REVERT: F 32 TYR cc_start: 0.8594 (m-80) cc_final: 0.8257 (m-80) REVERT: F 33 LEU cc_start: 0.2882 (OUTLIER) cc_final: 0.2559 (tm) REVERT: F 75 ILE cc_start: -0.0609 (OUTLIER) cc_final: -0.0821 (pt) REVERT: J 43 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7362 (tmtt) REVERT: J 46 GLU cc_start: 0.7302 (tp30) cc_final: 0.6765 (tp30) REVERT: J 108 MET cc_start: 0.5017 (tpt) cc_final: 0.4784 (mmm) REVERT: K 45 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7962 (mmm160) REVERT: K 104 VAL cc_start: -0.0198 (OUTLIER) cc_final: -0.0537 (t) outliers start: 40 outliers final: 20 residues processed: 126 average time/residue: 0.1887 time to fit residues: 39.1066 Evaluate side-chains 114 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 47 optimal weight: 0.5980 chunk 150 optimal weight: 0.0870 chunk 177 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 240 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 208 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.090394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055729 restraints weight = 126185.296| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.02 r_work: 0.3082 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30450 Z= 0.090 Angle : 0.476 9.527 41530 Z= 0.245 Chirality : 0.041 0.251 4783 Planarity : 0.003 0.052 5283 Dihedral : 3.532 16.932 4028 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.08 % Allowed : 12.58 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.65 (0.14), residues: 3679 helix: 2.01 (0.21), residues: 653 sheet: 0.93 (0.16), residues: 950 loop : -0.31 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1107 TYR 0.022 0.001 TYR C 369 PHE 0.016 0.001 PHE B 342 TRP 0.026 0.001 TRP A 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (30364) covalent geometry : angle 0.47109 / 0.24 (41317) SS BOND : bond 0.00195 / 0.12 ( 45) SS BOND : angle 0.61355 / 0.52 ( 90) hydrogen bonds : bond 0.02970 / 1.90 ( 1051) hydrogen bonds : angle 4.85003 / 3.38 ( 2958) link_BETA1-4 : bond 0.00329 / 0.26 ( 16) link_BETA1-4 : angle 1.14964 / 0.86 ( 48) link_NAG-ASN : bond 0.00136 / 0.08 ( 25) link_NAG-ASN : angle 1.43793 / 1.01 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: A 697 MET cc_start: 0.8431 (tmm) cc_final: 0.7651 (tmm) REVERT: B 770 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9127 (tt) REVERT: C 130 VAL cc_start: 0.6766 (OUTLIER) cc_final: 0.6414 (t) REVERT: C 731 MET cc_start: 0.8230 (ttt) cc_final: 0.7940 (ttm) REVERT: C 869 MET cc_start: 0.9430 (mtm) cc_final: 0.8980 (ttm) REVERT: C 1002 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8559 (tm-30) REVERT: H 3 GLN cc_start: 0.9414 (mm110) cc_final: 0.9111 (tm-30) REVERT: H 81 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8801 (mtmm) REVERT: L 17 GLU cc_start: 0.5403 (tm-30) cc_final: 0.4864 (pt0) REVERT: L 60 ASP cc_start: 0.8446 (m-30) cc_final: 0.7885 (m-30) REVERT: L 61 ARG cc_start: 0.8405 (mmp80) cc_final: 0.8173 (ptt180) REVERT: L 96 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: L 104 VAL cc_start: 0.4924 (OUTLIER) cc_final: 0.4677 (p) REVERT: E 51 MET cc_start: 0.5185 (OUTLIER) cc_final: 0.4923 (pmm) REVERT: E 77 GLN cc_start: 0.8184 (pp30) cc_final: 0.7745 (pp30) REVERT: E 108 MET cc_start: 0.7996 (tpt) cc_final: 0.6995 (pmm) REVERT: F 32 TYR cc_start: 0.8553 (m-80) cc_final: 0.8200 (m-80) REVERT: F 33 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2440 (tm) REVERT: F 75 ILE cc_start: -0.0415 (OUTLIER) cc_final: -0.0618 (pt) REVERT: J 43 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7433 (tmtt) REVERT: J 46 GLU cc_start: 0.7338 (tp30) cc_final: 0.6839 (tp30) REVERT: J 108 MET cc_start: 0.4996 (tpt) cc_final: 0.4764 (mmm) REVERT: K 45 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8215 (mmm160) REVERT: K 104 VAL cc_start: -0.0211 (OUTLIER) cc_final: -0.0551 (t) outliers start: 35 outliers final: 21 residues processed: 120 average time/residue: 0.2103 time to fit residues: 41.0869 Evaluate side-chains 116 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 12 optimal weight: 10.0000 chunk 140 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 992 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.096589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.062696 restraints weight = 143705.752| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.34 r_work: 0.3087 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30450 Z= 0.130 Angle : 0.490 9.546 41530 Z= 0.250 Chirality : 0.042 0.251 4783 Planarity : 0.003 0.052 5283 Dihedral : 3.558 16.499 4028 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.05 % Allowed : 12.64 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.68 (0.14), residues: 3679 helix: 2.04 (0.21), residues: 656 sheet: 0.88 (0.16), residues: 960 loop : -0.26 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.023 0.001 TYR C 369 PHE 0.015 0.001 PHE B 342 TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (30364) covalent geometry : angle 0.48365 / 0.25 (41317) SS BOND : bond 0.00220 / 0.15 ( 45) SS BOND : angle 0.66692 / 0.58 ( 90) hydrogen bonds : bond 0.03050 / 1.96 ( 1051) hydrogen bonds : angle 4.83590 / 3.37 ( 2958) link_BETA1-4 : bond 0.00183 / 0.15 ( 16) link_BETA1-4 : angle 1.25268 / 1.15 ( 48) link_NAG-ASN : bond 0.00208 / 0.16 ( 25) link_NAG-ASN : angle 1.60228 / 1.15 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: A 697 MET cc_start: 0.8394 (tmm) cc_final: 0.7607 (tmm) REVERT: B 770 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9148 (tt) REVERT: C 130 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.6529 (t) REVERT: C 731 MET cc_start: 0.8279 (ttt) cc_final: 0.7924 (ttt) REVERT: C 869 MET cc_start: 0.9367 (mtm) cc_final: 0.8927 (ttm) REVERT: H 3 GLN cc_start: 0.9474 (mm110) cc_final: 0.9112 (tm-30) REVERT: H 81 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8942 (mtmm) REVERT: L 60 ASP cc_start: 0.8383 (m-30) cc_final: 0.7759 (m-30) REVERT: L 61 ARG cc_start: 0.8292 (mmp80) cc_final: 0.8020 (ptt180) REVERT: L 96 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: L 104 VAL cc_start: 0.5507 (OUTLIER) cc_final: 0.5256 (p) REVERT: E 51 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5500 (pmm) REVERT: F 32 TYR cc_start: 0.8041 (m-80) cc_final: 0.7712 (m-80) REVERT: F 75 ILE cc_start: -0.0562 (OUTLIER) cc_final: -0.0807 (pt) REVERT: J 35 TRP cc_start: 0.8036 (m100) cc_final: 0.7191 (m100) REVERT: J 46 GLU cc_start: 0.7886 (tp30) cc_final: 0.7587 (tp30) REVERT: K 104 VAL cc_start: 0.1916 (OUTLIER) cc_final: 0.1678 (t) outliers start: 34 outliers final: 21 residues processed: 116 average time/residue: 0.1995 time to fit residues: 38.3461 Evaluate side-chains 112 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 195 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 196 optimal weight: 0.5980 chunk 306 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.095786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.062639 restraints weight = 143184.923| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.11 r_work: 0.3034 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30450 Z= 0.168 Angle : 0.519 9.550 41530 Z= 0.264 Chirality : 0.042 0.256 4783 Planarity : 0.004 0.109 5283 Dihedral : 3.706 18.990 4028 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.05 % Allowed : 12.79 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.14), residues: 3679 helix: 1.94 (0.21), residues: 661 sheet: 0.80 (0.16), residues: 963 loop : -0.24 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1091 TYR 0.023 0.001 TYR C 369 PHE 0.013 0.001 PHE C1121 TRP 0.019 0.001 TRP J 103 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (30364) covalent geometry : angle 0.51277 / 0.26 (41317) SS BOND : bond 0.00279 / 0.19 ( 45) SS BOND : angle 0.72160 / 0.65 ( 90) hydrogen bonds : bond 0.03168 / 2.04 ( 1051) hydrogen bonds : angle 4.91951 / 3.44 ( 2958) link_BETA1-4 : bond 0.00164 / 0.14 ( 16) link_BETA1-4 : angle 1.25102 / 1.14 ( 48) link_NAG-ASN : bond 0.00282 / 0.22 ( 25) link_NAG-ASN : angle 1.70605 / 1.23 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: A 697 MET cc_start: 0.8414 (tmm) cc_final: 0.7644 (tmm) REVERT: B 770 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9116 (tt) REVERT: C 130 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6467 (t) REVERT: C 731 MET cc_start: 0.8332 (ttt) cc_final: 0.7930 (ttt) REVERT: C 869 MET cc_start: 0.9426 (mtm) cc_final: 0.8975 (ttm) REVERT: L 96 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7994 (mm-40) REVERT: L 104 VAL cc_start: 0.5320 (OUTLIER) cc_final: 0.5058 (p) REVERT: E 51 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.5359 (pmm) REVERT: E 108 MET cc_start: 0.8000 (tpt) cc_final: 0.7502 (pmm) REVERT: F 32 TYR cc_start: 0.8334 (m-80) cc_final: 0.7974 (m-80) REVERT: F 75 ILE cc_start: -0.0684 (OUTLIER) cc_final: -0.0927 (pt) REVERT: J 35 TRP cc_start: 0.7908 (m100) cc_final: 0.6915 (m100) REVERT: J 43 LYS cc_start: 0.7029 (tmtt) cc_final: 0.6628 (mmmt) REVERT: K 104 VAL cc_start: 0.0730 (OUTLIER) cc_final: 0.0451 (t) outliers start: 34 outliers final: 20 residues processed: 111 average time/residue: 0.1821 time to fit residues: 34.0440 Evaluate side-chains 107 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 184 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 368 optimal weight: 30.0000 chunk 351 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 339 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 363 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.095894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.062216 restraints weight = 143629.590| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 5.54 r_work: 0.3074 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30450 Z= 0.144 Angle : 0.512 11.538 41530 Z= 0.259 Chirality : 0.042 0.252 4783 Planarity : 0.003 0.052 5283 Dihedral : 3.686 17.257 4028 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.92 % Allowed : 13.13 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.64 (0.14), residues: 3679 helix: 1.92 (0.21), residues: 662 sheet: 0.82 (0.16), residues: 936 loop : -0.22 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.023 0.001 TYR C 369 PHE 0.011 0.001 PHE B1121 TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (30364) covalent geometry : angle 0.50559 / 0.26 (41317) SS BOND : bond 0.00233 / 0.16 ( 45) SS BOND : angle 0.66695 / 0.59 ( 90) hydrogen bonds : bond 0.03089 / 1.98 ( 1051) hydrogen bonds : angle 4.89433 / 3.42 ( 2958) link_BETA1-4 : bond 0.00194 / 0.17 ( 16) link_BETA1-4 : angle 1.19621 / 1.02 ( 48) link_NAG-ASN : bond 0.00212 / 0.17 ( 25) link_NAG-ASN : angle 1.63572 / 1.18 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10041.98 seconds wall clock time: 172 minutes 5.49 seconds (10325.49 seconds total)