Starting phenix.real_space_refine on Fri Mar 6 09:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5h_24190/03_2026/7n5h_24190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5h_24190/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n5h_24190/03_2026/7n5h_24190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5h_24190/03_2026/7n5h_24190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n5h_24190/03_2026/7n5h_24190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5h_24190/03_2026/7n5h_24190.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.30, per 1000 atoms: 0.21 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: 2.23 Conformation dependent library (CDL) restraints added in 1.4 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: 1.28 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: 8.03 Time building geometry restraints manager: 3.06 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: 17038 17.86 - 35.72: 1227 35.72 - 53.58: 239 53.58 - 71.44: 55 71.44 - 89.30: 25 Dihedral angle restraints: 18584 sinusoidal: 7724 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 18581 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: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.680 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.160 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 12.671 89.302 11487 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 covalent geometry : bond 0.00853 (30364) covalent geometry : angle 1.18708 (41317) SS BOND : bond 0.02873 ( 45) SS BOND : angle 1.64377 ( 90) hydrogen bonds : bond 0.25908 ( 1051) hydrogen bonds : angle 9.83780 ( 2958) link_BETA1-4 : bond 0.00722 ( 16) link_BETA1-4 : angle 2.10438 ( 48) link_NAG-ASN : bond 0.00321 ( 25) link_NAG-ASN : angle 2.55237 ( 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 : 0.994 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: 0.1935 time to fit residues: 90.5835 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 : 0.913 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 414 GLN A 422 ASN A 450 ASN A 498 GLN 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 = 0.4097 r_free = 0.4097 target = 0.092918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.058853 restraints weight = 129111.520| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.06 r_work: 0.3154 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 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 = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30450 Z= 0.171 Angle : 0.601 9.903 41530 Z= 0.316 Chirality : 0.043 0.264 4783 Planarity : 0.004 0.066 5283 Dihedral : 5.451 56.714 4890 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.77 % Allowed : 8.67 % Favored : 90.56 % 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: -0.39 (0.13), residues: 3679 helix: 0.21 (0.19), residues: 657 sheet: 0.53 (0.16), residues: 953 loop : -0.78 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.024 0.002 TYR J 53 PHE 0.024 0.001 PHE A 338 TRP 0.015 0.002 TRP J 103 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00380 (30364) covalent geometry : angle 0.59368 (41317) SS BOND : bond 0.00319 ( 45) SS BOND : angle 0.93355 ( 90) hydrogen bonds : bond 0.05059 ( 1051) hydrogen bonds : angle 6.45444 ( 2958) link_BETA1-4 : bond 0.00312 ( 16) link_BETA1-4 : angle 1.32930 ( 48) link_NAG-ASN : bond 0.00290 ( 25) link_NAG-ASN : angle 1.96173 ( 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 165 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.283 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 751 ASN cc_start: 0.9043 (m-40) cc_final: 0.8523 (m-40) REVERT: C 338 PHE cc_start: 0.7764 (m-10) cc_final: 0.7530 (m-10) REVERT: C 731 MET cc_start: 0.7963 (ttt) cc_final: 0.7723 (ttt) REVERT: L 17 GLU cc_start: 0.3730 (tm-30) cc_final: 0.3229 (tt0) REVERT: E 87 THR cc_start: -0.0401 (OUTLIER) cc_final: -0.1349 (t) REVERT: E 108 MET cc_start: 0.7874 (tpt) cc_final: 0.7024 (pmm) outliers start: 25 outliers final: 11 residues processed: 162 average time/residue: 0.2128 time to fit residues: 53.2176 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 : 0.960 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 253 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 414 GLN B 450 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 37 GLN 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 = 0.4019 r_free = 0.4019 target = 0.089473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053479 restraints weight = 121747.071| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.17 r_work: 0.2973 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 30450 Z= 0.333 Angle : 0.714 11.009 41530 Z= 0.366 Chirality : 0.047 0.260 4783 Planarity : 0.005 0.064 5283 Dihedral : 5.582 56.806 4890 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 10.76 % Favored : 87.88 % 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: -0.09 (0.13), residues: 3679 helix: 1.02 (0.20), residues: 655 sheet: 0.33 (0.16), residues: 959 loop : -0.57 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 61 TYR 0.021 0.002 TYR J 53 PHE 0.031 0.002 PHE A 906 TRP 0.032 0.002 TRP J 35A HIS 0.008 0.002 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00747 (30364) covalent geometry : angle 0.70128 (41317) SS BOND : bond 0.00444 ( 45) SS BOND : angle 1.17768 ( 90) hydrogen bonds : bond 0.04648 ( 1051) hydrogen bonds : angle 6.02525 ( 2958) link_BETA1-4 : bond 0.00391 ( 16) link_BETA1-4 : angle 1.84340 ( 48) link_NAG-ASN : bond 0.00880 ( 25) link_NAG-ASN : angle 2.68789 ( 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 152 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1019 ARG cc_start: 0.9245 (tpp-160) cc_final: 0.8961 (tpt170) REVERT: B 1050 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8662 (ptp) REVERT: C 338 PHE cc_start: 0.7937 (m-10) cc_final: 0.7535 (m-10) REVERT: C 731 MET cc_start: 0.8459 (ttt) cc_final: 0.8119 (ttt) REVERT: C 869 MET cc_start: 0.9477 (mtm) cc_final: 0.9245 (mtm) REVERT: H 81 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8878 (mtmm) REVERT: H 100 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: L 17 GLU cc_start: 0.5215 (tm-30) cc_final: 0.4879 (tt0) REVERT: L 49 TYR cc_start: 0.8676 (p90) cc_final: 0.8434 (p90) REVERT: L 96 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: E 77 GLN cc_start: 0.7916 (pp30) cc_final: 0.7335 (pp30) REVERT: E 87 THR cc_start: -0.0700 (OUTLIER) cc_final: -0.1752 (t) REVERT: E 108 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7044 (pmm) REVERT: F 33 LEU cc_start: 0.3048 (OUTLIER) cc_final: 0.2734 (tm) REVERT: F 37 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: F 47 LEU cc_start: 0.7570 (tt) cc_final: 0.6357 (tp) REVERT: J 38 ARG cc_start: 0.6527 (ptt-90) cc_final: 0.6206 (ptt-90) REVERT: J 43 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7492 (tmtt) REVERT: J 108 MET cc_start: 0.5173 (tpt) cc_final: 0.4940 (mmm) REVERT: K 45 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7919 (mmm160) outliers start: 44 outliers final: 14 residues processed: 141 average time/residue: 0.1802 time to fit residues: 41.3765 Evaluate side-chains 102 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 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 242 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 C residue 505 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 102 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 37 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 37 GLN 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: 9.9990 chunk 6 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 356 optimal weight: 40.0000 chunk 135 optimal weight: 30.0000 chunk 357 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 965 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 77 GLN L 37 GLN L 42 GLN E 3 GLN F 37 GLN K 27 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.088989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.053744 restraints weight = 123812.276| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.02 r_work: 0.3027 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30450 Z= 0.262 Angle : 0.604 9.729 41530 Z= 0.310 Chirality : 0.045 0.237 4783 Planarity : 0.004 0.101 5283 Dihedral : 5.376 56.230 4890 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.48 % Allowed : 11.90 % Favored : 86.62 % 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: 0.04 (0.13), residues: 3679 helix: 1.46 (0.20), residues: 648 sheet: 0.23 (0.16), residues: 963 loop : -0.51 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.020 0.001 TYR B 904 PHE 0.020 0.002 PHE F 62 TRP 0.027 0.002 TRP J 35A HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00590 (30364) covalent geometry : angle 0.59404 (41317) SS BOND : bond 0.00387 ( 45) SS BOND : angle 1.13744 ( 90) hydrogen bonds : bond 0.03819 ( 1051) hydrogen bonds : angle 5.76918 ( 2958) link_BETA1-4 : bond 0.00186 ( 16) link_BETA1-4 : angle 1.42313 ( 48) link_NAG-ASN : bond 0.00428 ( 25) link_NAG-ASN : angle 2.17037 ( 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 142 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 0.979 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 368 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8891 (mp) REVERT: C 731 MET cc_start: 0.8408 (ttt) cc_final: 0.8042 (ttt) REVERT: C 869 MET cc_start: 0.9402 (mtm) cc_final: 0.8935 (ttm) REVERT: C 1136 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9353 (p) REVERT: H 81 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8785 (mtmm) REVERT: H 100 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8442 (m-10) REVERT: L 17 GLU cc_start: 0.5214 (tm-30) cc_final: 0.4895 (tt0) REVERT: L 49 TYR cc_start: 0.8649 (p90) cc_final: 0.8421 (p90) REVERT: L 104 VAL cc_start: 0.5147 (OUTLIER) cc_final: 0.4841 (p) REVERT: E 77 GLN cc_start: 0.7953 (pp30) cc_final: 0.7365 (pp30) REVERT: E 87 THR cc_start: -0.0760 (OUTLIER) cc_final: -0.1631 (t) REVERT: E 108 MET cc_start: 0.7896 (tpt) cc_final: 0.6871 (pmm) REVERT: F 33 LEU cc_start: 0.3683 (OUTLIER) cc_final: 0.3326 (tm) REVERT: F 37 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: F 47 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6144 (mt) REVERT: J 108 MET cc_start: 0.5281 (tpt) cc_final: 0.5000 (mmm) REVERT: K 45 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7706 (mmm160) outliers start: 48 outliers final: 19 residues processed: 132 average time/residue: 0.1822 time to fit residues: 39.1038 Evaluate side-chains 109 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 113 LYS 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 B residue 1050 MET Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 69 THR 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 F residue 33 LEU Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU 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: 5.9990 chunk 321 optimal weight: 0.0980 chunk 274 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 299 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 935 GLN C 992 GLN H 3 GLN H 5 GLN F 37 GLN K 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.090123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055211 restraints weight = 126866.042| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.05 r_work: 0.3079 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30450 Z= 0.110 Angle : 0.513 9.621 41530 Z= 0.264 Chirality : 0.042 0.242 4783 Planarity : 0.003 0.059 5283 Dihedral : 4.937 56.266 4889 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.41 % Allowed : 12.58 % Favored : 86.01 % 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: 0.26 (0.13), residues: 3679 helix: 1.69 (0.20), residues: 652 sheet: 0.43 (0.16), residues: 940 loop : -0.41 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.020 0.001 TYR C 369 PHE 0.034 0.001 PHE B 342 TRP 0.028 0.001 TRP J 35A HIS 0.002 0.000 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00249 (30364) covalent geometry : angle 0.50606 (41317) SS BOND : bond 0.00254 ( 45) SS BOND : angle 0.74655 ( 90) hydrogen bonds : bond 0.03349 ( 1051) hydrogen bonds : angle 5.38866 ( 2958) link_BETA1-4 : bond 0.00302 ( 16) link_BETA1-4 : angle 1.26295 ( 48) link_NAG-ASN : bond 0.00177 ( 25) link_NAG-ASN : angle 1.71383 ( 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 142 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: B 770 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9149 (tt) REVERT: C 731 MET cc_start: 0.8265 (ttt) cc_final: 0.7878 (ttt) REVERT: C 869 MET cc_start: 0.9375 (mtm) cc_final: 0.8926 (ttm) REVERT: H 3 GLN cc_start: 0.9414 (mm110) cc_final: 0.9106 (tp40) REVERT: H 72 ASP cc_start: 0.9173 (m-30) cc_final: 0.8308 (t0) REVERT: H 81 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8765 (mtmm) REVERT: H 100 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: L 17 GLU cc_start: 0.5335 (tm-30) cc_final: 0.5076 (tt0) REVERT: L 49 TYR cc_start: 0.8627 (p90) cc_final: 0.8418 (p90) REVERT: L 104 VAL cc_start: 0.4957 (OUTLIER) cc_final: 0.4690 (p) REVERT: E 51 MET cc_start: 0.4886 (ppp) cc_final: 0.4556 (pmm) REVERT: E 77 GLN cc_start: 0.8056 (pp30) cc_final: 0.7513 (pp30) REVERT: E 87 THR cc_start: -0.0847 (OUTLIER) cc_final: -0.1597 (t) REVERT: E 108 MET cc_start: 0.7774 (tpt) cc_final: 0.6909 (pmm) REVERT: F 32 TYR cc_start: 0.8756 (m-10) cc_final: 0.8519 (m-80) REVERT: F 33 LEU cc_start: 0.3412 (OUTLIER) cc_final: 0.3007 (tm) REVERT: F 47 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.5623 (mt) REVERT: J 43 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6994 (tmtt) REVERT: J 108 MET cc_start: 0.5044 (tpt) cc_final: 0.4514 (mmm) REVERT: K 45 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7919 (mmm160) REVERT: K 104 VAL cc_start: -0.0794 (OUTLIER) cc_final: -0.1145 (t) outliers start: 46 outliers final: 19 residues processed: 131 average time/residue: 0.1778 time to fit residues: 38.5582 Evaluate side-chains 107 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 1104 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 324 GLU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain H residue 100 TYR 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 107 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 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 Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 31 optimal weight: 0.0970 chunk 269 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 160 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 762 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 = 0.4048 r_free = 0.4048 target = 0.090232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055721 restraints weight = 128153.857| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.74 r_work: 0.3078 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4293 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= 0.105 Angle : 0.497 9.597 41530 Z= 0.256 Chirality : 0.042 0.243 4783 Planarity : 0.003 0.057 5283 Dihedral : 4.706 56.310 4889 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.45 % Allowed : 12.79 % Favored : 85.76 % 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: 1.83 (0.21), residues: 653 sheet: 0.59 (0.16), residues: 935 loop : -0.36 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 54 TYR 0.023 0.001 TYR C 369 PHE 0.022 0.001 PHE F 62 TRP 0.043 0.001 TRP J 35A HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00235 (30364) covalent geometry : angle 0.49089 (41317) SS BOND : bond 0.00216 ( 45) SS BOND : angle 0.62713 ( 90) hydrogen bonds : bond 0.03142 ( 1051) hydrogen bonds : angle 5.13245 ( 2958) link_BETA1-4 : bond 0.00234 ( 16) link_BETA1-4 : angle 1.27480 ( 48) link_NAG-ASN : bond 0.00128 ( 25) link_NAG-ASN : angle 1.63840 ( 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 136 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 89 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: A 699 LEU cc_start: 0.8803 (mt) cc_final: 0.8526 (mt) REVERT: B 770 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9140 (tt) REVERT: C 130 VAL cc_start: 0.6732 (OUTLIER) cc_final: 0.6400 (t) REVERT: C 731 MET cc_start: 0.8251 (ttt) cc_final: 0.7932 (ttm) REVERT: C 869 MET cc_start: 0.9415 (mtm) cc_final: 0.8955 (ttm) REVERT: H 3 GLN cc_start: 0.9245 (mm110) cc_final: 0.9019 (mm-40) REVERT: H 72 ASP cc_start: 0.9168 (m-30) cc_final: 0.8234 (t0) REVERT: H 81 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8711 (mtmm) REVERT: H 100 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: L 17 GLU cc_start: 0.5451 (tm-30) cc_final: 0.5234 (tt0) REVERT: L 104 VAL cc_start: 0.4978 (OUTLIER) cc_final: 0.4701 (p) REVERT: E 51 MET cc_start: 0.5152 (ppp) cc_final: 0.4865 (pmm) REVERT: E 77 GLN cc_start: 0.8071 (pp30) cc_final: 0.7498 (pp30) REVERT: E 87 THR cc_start: -0.0603 (OUTLIER) cc_final: -0.1272 (t) REVERT: E 108 MET cc_start: 0.7595 (tpt) cc_final: 0.6819 (pmm) REVERT: F 32 TYR cc_start: 0.8711 (m-10) cc_final: 0.8409 (m-80) REVERT: F 33 LEU cc_start: 0.3563 (OUTLIER) cc_final: 0.3144 (tm) REVERT: J 43 LYS cc_start: 0.7428 (mmmt) cc_final: 0.7084 (tmtt) REVERT: J 108 MET cc_start: 0.5201 (tpt) cc_final: 0.4889 (mmm) REVERT: K 45 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7975 (mmm160) outliers start: 47 outliers final: 22 residues processed: 131 average time/residue: 0.1777 time to fit residues: 38.3922 Evaluate side-chains 111 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 C residue 878 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 24 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.088924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054256 restraints weight = 126641.343| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.94 r_work: 0.3046 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 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 = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30450 Z= 0.186 Angle : 0.537 9.608 41530 Z= 0.274 Chirality : 0.043 0.246 4783 Planarity : 0.003 0.055 5283 Dihedral : 4.794 56.424 4889 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.57 % Allowed : 12.82 % Favored : 85.61 % 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: 1.80 (0.21), residues: 661 sheet: 0.54 (0.16), residues: 944 loop : -0.32 (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 0.033 0.001 PHE B 342 TRP 0.020 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00422 (30364) covalent geometry : angle 0.52919 (41317) SS BOND : bond 0.00296 ( 45) SS BOND : angle 0.71211 ( 90) hydrogen bonds : bond 0.03292 ( 1051) hydrogen bonds : angle 5.14999 ( 2958) link_BETA1-4 : bond 0.00127 ( 16) link_BETA1-4 : angle 1.38153 ( 48) link_NAG-ASN : bond 0.00353 ( 25) link_NAG-ASN : angle 1.87561 ( 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 137 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 86 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: B 770 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9156 (tt) REVERT: C 130 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6543 (t) REVERT: C 731 MET cc_start: 0.8323 (ttt) cc_final: 0.7912 (ttt) REVERT: C 869 MET cc_start: 0.9375 (mtm) cc_final: 0.8908 (ttm) REVERT: H 81 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8778 (mtmm) REVERT: H 100 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: L 17 GLU cc_start: 0.5468 (tm-30) cc_final: 0.4951 (pt0) REVERT: L 61 ARG cc_start: 0.8501 (mmp80) cc_final: 0.8098 (ptt180) REVERT: L 104 VAL cc_start: 0.5133 (OUTLIER) cc_final: 0.4834 (p) REVERT: E 51 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4855 (pmm) REVERT: E 77 GLN cc_start: 0.8224 (pp30) cc_final: 0.7820 (pp30) REVERT: E 87 THR cc_start: -0.1088 (OUTLIER) cc_final: -0.1859 (t) REVERT: E 108 MET cc_start: 0.7589 (tpt) cc_final: 0.6957 (pmm) REVERT: F 32 TYR cc_start: 0.8743 (m-10) cc_final: 0.8475 (m-80) REVERT: F 33 LEU cc_start: 0.3188 (OUTLIER) cc_final: 0.2795 (tm) REVERT: J 43 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7109 (tmtt) REVERT: J 108 MET cc_start: 0.5262 (tpt) cc_final: 0.5058 (mmm) REVERT: K 104 VAL cc_start: -0.0541 (OUTLIER) cc_final: -0.0795 (t) outliers start: 51 outliers final: 31 residues processed: 129 average time/residue: 0.1706 time to fit residues: 36.9098 Evaluate side-chains 119 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 350 VAL 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 767 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 362 VAL 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 C residue 878 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 THR 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 87 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 102 ILE 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 56 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 47 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 307 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 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 = 0.4027 r_free = 0.4027 target = 0.088681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.053660 restraints weight = 126637.697| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.02 r_work: 0.3028 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 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 = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30450 Z= 0.203 Angle : 0.546 9.633 41530 Z= 0.278 Chirality : 0.043 0.247 4783 Planarity : 0.003 0.054 5283 Dihedral : 4.897 56.588 4889 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.63 % Allowed : 13.04 % Favored : 85.33 % 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: 0.38 (0.14), residues: 3679 helix: 1.79 (0.21), residues: 661 sheet: 0.46 (0.16), residues: 954 loop : -0.32 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.021 0.001 TYR C 369 PHE 0.017 0.001 PHE B 342 TRP 0.022 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00457 (30364) covalent geometry : angle 0.53777 (41317) SS BOND : bond 0.00300 ( 45) SS BOND : angle 0.73055 ( 90) hydrogen bonds : bond 0.03371 ( 1051) hydrogen bonds : angle 5.18063 ( 2958) link_BETA1-4 : bond 0.00139 ( 16) link_BETA1-4 : angle 1.34887 ( 48) link_NAG-ASN : bond 0.00365 ( 25) link_NAG-ASN : angle 1.92456 ( 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 139 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 86 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: B 770 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 1019 ARG cc_start: 0.9121 (tpp-160) cc_final: 0.8902 (tpp-160) REVERT: C 130 VAL cc_start: 0.6780 (OUTLIER) cc_final: 0.6458 (t) REVERT: C 731 MET cc_start: 0.8334 (ttt) cc_final: 0.7911 (ttt) REVERT: C 869 MET cc_start: 0.9385 (mtm) cc_final: 0.8899 (ttm) REVERT: H 81 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8759 (mtmm) REVERT: H 100 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8528 (m-10) REVERT: L 17 GLU cc_start: 0.5538 (tm-30) cc_final: 0.5055 (pt0) REVERT: L 61 ARG cc_start: 0.8472 (mmp80) cc_final: 0.8094 (ptt180) REVERT: L 104 VAL cc_start: 0.5264 (OUTLIER) cc_final: 0.4961 (p) REVERT: E 51 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5185 (pmm) REVERT: E 77 GLN cc_start: 0.8171 (pp30) cc_final: 0.7803 (pp30) REVERT: E 87 THR cc_start: -0.1085 (OUTLIER) cc_final: -0.1883 (t) REVERT: E 108 MET cc_start: 0.7581 (tpt) cc_final: 0.6999 (pmm) REVERT: F 32 TYR cc_start: 0.8780 (m-10) cc_final: 0.8514 (m-80) REVERT: F 33 LEU cc_start: 0.3180 (OUTLIER) cc_final: 0.2783 (tm) REVERT: J 35 TRP cc_start: 0.7440 (m100) cc_final: 0.7065 (m100) REVERT: J 43 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7127 (tmtt) REVERT: J 108 MET cc_start: 0.5229 (tpt) cc_final: 0.5014 (mmm) REVERT: K 104 VAL cc_start: 0.0055 (OUTLIER) cc_final: -0.0290 (t) outliers start: 53 outliers final: 36 residues processed: 132 average time/residue: 0.1706 time to fit residues: 37.9246 Evaluate side-chains 127 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 82 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 350 VAL 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 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 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 760 CYS 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 C residue 714 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE 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 87 THR Chi-restraints excluded: chain E residue 89 VAL 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 56 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 12 optimal weight: 0.0770 chunk 140 optimal weight: 0.0070 chunk 67 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B 115 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** J 77 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 = 0.4043 r_free = 0.4043 target = 0.090385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055118 restraints weight = 128319.322| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.81 r_work: 0.3062 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 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 = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30450 Z= 0.096 Angle : 0.499 9.602 41530 Z= 0.256 Chirality : 0.042 0.325 4783 Planarity : 0.003 0.055 5283 Dihedral : 4.692 56.593 4889 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 13.35 % Favored : 85.39 % 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: 1.90 (0.21), residues: 659 sheet: 0.67 (0.16), residues: 919 loop : -0.29 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.022 0.001 TYR C 369 PHE 0.014 0.001 PHE B 342 TRP 0.027 0.001 TRP A 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00219 (30364) covalent geometry : angle 0.49337 (41317) SS BOND : bond 0.00212 ( 45) SS BOND : angle 0.56642 ( 90) hydrogen bonds : bond 0.03031 ( 1051) hydrogen bonds : angle 4.97723 ( 2958) link_BETA1-4 : bond 0.00310 ( 16) link_BETA1-4 : angle 1.21413 ( 48) link_NAG-ASN : bond 0.00138 ( 25) link_NAG-ASN : angle 1.61471 ( 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 126 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8559 (mp10) REVERT: A 699 LEU cc_start: 0.8807 (mt) cc_final: 0.8510 (mt) REVERT: B 770 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9095 (tt) REVERT: C 130 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6245 (t) REVERT: C 731 MET cc_start: 0.8272 (ttt) cc_final: 0.7894 (ttt) REVERT: C 869 MET cc_start: 0.9400 (mtm) cc_final: 0.8929 (ttm) REVERT: C 1128 VAL cc_start: 0.9543 (m) cc_final: 0.9333 (p) REVERT: H 1 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7291 (pm20) REVERT: H 3 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8961 (tp40) REVERT: H 81 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8728 (mtmm) REVERT: H 100 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8360 (m-10) REVERT: L 17 GLU cc_start: 0.5646 (tm-30) cc_final: 0.5241 (pt0) REVERT: L 61 ARG cc_start: 0.8493 (mmp80) cc_final: 0.8209 (ptt180) REVERT: L 104 VAL cc_start: 0.5031 (OUTLIER) cc_final: 0.4739 (p) REVERT: E 51 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5534 (pmm) REVERT: E 77 GLN cc_start: 0.8167 (pp30) cc_final: 0.7668 (pp30) REVERT: E 87 THR cc_start: -0.0932 (OUTLIER) cc_final: -0.1501 (t) REVERT: E 108 MET cc_start: 0.7542 (tpt) cc_final: 0.6751 (pmm) REVERT: F 32 TYR cc_start: 0.8730 (m-10) cc_final: 0.8462 (m-80) REVERT: F 33 LEU cc_start: 0.3604 (OUTLIER) cc_final: 0.3182 (tm) REVERT: J 3 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8527 (tp-100) REVERT: J 35 TRP cc_start: 0.7284 (m100) cc_final: 0.6858 (m100) REVERT: J 43 LYS cc_start: 0.7313 (mmmt) cc_final: 0.7015 (tmtt) REVERT: J 108 MET cc_start: 0.5218 (tpt) cc_final: 0.4984 (mmm) REVERT: K 104 VAL cc_start: -0.0091 (OUTLIER) cc_final: -0.0409 (t) outliers start: 41 outliers final: 28 residues processed: 119 average time/residue: 0.1695 time to fit residues: 33.9388 Evaluate side-chains 115 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 350 VAL 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 723 THR 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 327 VAL 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 760 CYS 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 C residue 714 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE 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 89 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 195 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 44 optimal weight: 0.0870 chunk 134 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 5 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 = 0.4038 r_free = 0.4038 target = 0.089402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055190 restraints weight = 127073.423| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.69 r_work: 0.3056 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 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 = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4790 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= 0.119 Angle : 0.495 9.604 41530 Z= 0.254 Chirality : 0.042 0.246 4783 Planarity : 0.003 0.055 5283 Dihedral : 4.640 56.474 4889 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.29 % Allowed : 13.38 % Favored : 85.33 % 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: 0.55 (0.14), residues: 3679 helix: 1.95 (0.21), residues: 660 sheet: 0.64 (0.16), residues: 931 loop : -0.25 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.021 0.001 TYR C 369 PHE 0.012 0.001 PHE B 342 TRP 0.024 0.001 TRP A 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00272 (30364) covalent geometry : angle 0.48855 (41317) SS BOND : bond 0.00227 ( 45) SS BOND : angle 0.57552 ( 90) hydrogen bonds : bond 0.03037 ( 1051) hydrogen bonds : angle 4.92272 ( 2958) link_BETA1-4 : bond 0.00216 ( 16) link_BETA1-4 : angle 1.25785 ( 48) link_NAG-ASN : bond 0.00153 ( 25) link_NAG-ASN : angle 1.66443 ( 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 127 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: A 699 LEU cc_start: 0.8808 (mt) cc_final: 0.8525 (mt) REVERT: B 770 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9090 (tt) REVERT: C 130 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6195 (t) REVERT: C 731 MET cc_start: 0.8260 (ttt) cc_final: 0.7964 (ttm) REVERT: C 869 MET cc_start: 0.9454 (mtm) cc_final: 0.8989 (ttm) REVERT: H 3 GLN cc_start: 0.9287 (mm110) cc_final: 0.8822 (tp40) REVERT: H 81 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8734 (mtmm) REVERT: H 100 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: L 17 GLU cc_start: 0.5649 (tm-30) cc_final: 0.5285 (pt0) REVERT: L 61 ARG cc_start: 0.8570 (mmp80) cc_final: 0.8288 (ptt180) REVERT: L 104 VAL cc_start: 0.5049 (OUTLIER) cc_final: 0.4760 (p) REVERT: E 51 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5557 (pmm) REVERT: E 77 GLN cc_start: 0.8181 (pp30) cc_final: 0.7682 (pp30) REVERT: E 87 THR cc_start: -0.0502 (OUTLIER) cc_final: -0.1049 (t) REVERT: E 108 MET cc_start: 0.7547 (tpt) cc_final: 0.6775 (pmm) REVERT: F 24 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8659 (mpt180) REVERT: F 32 TYR cc_start: 0.8749 (m-10) cc_final: 0.8480 (m-80) REVERT: F 33 LEU cc_start: 0.3451 (OUTLIER) cc_final: 0.3019 (tm) REVERT: J 3 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8559 (tp-100) REVERT: J 35 TRP cc_start: 0.7295 (m100) cc_final: 0.6895 (m100) REVERT: J 43 LYS cc_start: 0.7318 (mmmt) cc_final: 0.7021 (tmtt) REVERT: J 108 MET cc_start: 0.5166 (tpt) cc_final: 0.4932 (mmm) REVERT: K 104 VAL cc_start: 0.0002 (OUTLIER) cc_final: -0.0319 (t) outliers start: 42 outliers final: 31 residues processed: 121 average time/residue: 0.1777 time to fit residues: 36.1593 Evaluate side-chains 123 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 350 VAL 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 723 THR 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 760 CYS 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 C residue 714 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 106 ILE 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 89 VAL 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 37 GLN 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: 2.9990 chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 351 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 339 optimal weight: 40.0000 chunk 66 optimal weight: 0.9990 chunk 363 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 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 = 0.4038 r_free = 0.4038 target = 0.089217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054806 restraints weight = 127141.940| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.93 r_work: 0.3055 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 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 = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 30450 Z= 0.187 Angle : 0.648 58.852 41530 Z= 0.353 Chirality : 0.043 0.249 4783 Planarity : 0.003 0.055 5283 Dihedral : 4.638 56.476 4889 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.38 % Allowed : 13.44 % Favored : 85.18 % Cbeta Deviations : 0.03 % 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: 0.54 (0.14), residues: 3679 helix: 1.93 (0.21), residues: 660 sheet: 0.64 (0.16), residues: 931 loop : -0.25 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 38 TYR 0.021 0.001 TYR C 369 PHE 0.013 0.001 PHE B 342 TRP 0.021 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00412 (30364) covalent geometry : angle 0.64339 (41317) SS BOND : bond 0.00253 ( 45) SS BOND : angle 0.55629 ( 90) hydrogen bonds : bond 0.03172 ( 1051) hydrogen bonds : angle 4.92452 ( 2958) link_BETA1-4 : bond 0.00285 ( 16) link_BETA1-4 : angle 1.27300 ( 48) link_NAG-ASN : bond 0.00178 ( 25) link_NAG-ASN : angle 1.65984 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9496.51 seconds wall clock time: 162 minutes 40.54 seconds (9760.54 seconds total)