Starting phenix.real_space_refine on Sat Mar 7 00:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.map" model { file = "/net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c2l_30276/03_2026/7c2l_30276.cif" } resolution = 3.1 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= 0.004 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 158 5.16 5 C 22777 2.51 5 N 5872 2.21 5 O 7181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s 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: 35988 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8269 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 51, 'TRANS': 1003} Chain breaks: 7 Chain: "C" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8227 Classifications: {'peptide': 1049} Link IDs: {'PTRANS': 52, 'TRANS': 996} Chain breaks: 6 Chain: "H" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "L" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "I" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "M" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "J" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "N" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "D" 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 Chain: "E" 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 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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 Chain: "T" 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 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: "Z" 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: 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: "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 Chain: "d" 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 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.89, per 1000 atoms: 0.22 Number of scatterers: 35988 At special positions: 0 Unit cell: (229.357, 209.791, 228.27, 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 158 16.00 O 7181 8.00 N 5872 7.00 C 22777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.86 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.14 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.00 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=2.11 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=1.98 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.86 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.92 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.76 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=1.86 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.91 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.82 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=2.01 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=2.18 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.13 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.13 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 199 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " distance=2.13 Simple disulfide: pdb=" SG CYS N 139 " - pdb=" SG CYS N 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 S 2 " - " NAG S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " NAG T 3 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " NAG c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 61 " " NAG A1406 " - " ASN A 149 " " NAG A1414 " - " ASN A 331 " " NAG A1415 " - " ASN A 343 " " NAG A1416 " - " ASN A 603 " " NAG A1417 " - " ASN A 616 " " NAG A1418 " - " ASN A 657 " " NAG A1419 " - " ASN A 709 " " NAG B1401 " - " ASN B 17 " " NAG B1402 " - " ASN B 61 " " NAG B1406 " - " ASN B 149 " " NAG B1414 " - " ASN B 331 " " NAG B1415 " - " ASN B 343 " " NAG B1416 " - " ASN B 603 " " NAG B1417 " - " ASN B 616 " " NAG B1418 " - " ASN B 657 " " NAG C1401 " - " ASN C 17 " " NAG C1402 " - " ASN C 61 " " NAG C1406 " - " ASN C 149 " " NAG C1414 " - " ASN C 331 " " NAG C1415 " - " ASN C 343 " " NAG C1416 " - " ASN C 603 " " NAG C1417 " - " ASN C 616 " " NAG C1418 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 165 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 165 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 282 " " NAG g 1 " - " ASN C 709 " " NAG h 1 " - " ASN C 717 " " NAG i 1 " - " ASN C 801 " " NAG j 1 " - " ASN C1074 " " NAG k 1 " - " ASN C1098 " " NAG l 1 " - " ASN C1134 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8362 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 79 sheets defined 17.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.417A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.652A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.992A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.650A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.017A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.956A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.534A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.773A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.114A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.509A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.313A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.566A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.566A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (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 982 removed outlier: 3.910A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1026 removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.584A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.615A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.662A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.732A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.572A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.598A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.612A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.568A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.567A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.697A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.549A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.913A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.640A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 985 through 1034 removed outlier: 3.603A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.575A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.597A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.023A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.028A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.660A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.504A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.584A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.539A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 879 Processing helix chain 'C' and resid 879 through 884 removed outlier: 3.747A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.664A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.588A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.729A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.931A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A 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 983 removed outlier: 3.521A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.689A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.894A pdb=" N GLU L 192 " --> pdb=" O LYS L 188 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'M' and resid 187 through 193 removed outlier: 3.894A pdb=" N GLU M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'N' and resid 187 through 193 removed outlier: 3.893A pdb=" N GLU N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS N 193 " --> pdb=" O ALA N 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.397A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.593A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.105A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.770A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.696A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.505A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.562A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.514A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.790A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.013A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.776A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.593A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.860A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.892A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.515A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.829A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.096A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.000A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.575A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.408A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.592A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.270A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF2, first strand: chain 'C' and resid 551 through 554 removed outlier: 3.510A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.971A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR H 122 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 99 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR H 122 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL H 196 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS H 179 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 209 through 215 removed outlier: 4.596A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.882A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.651A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.937A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL L 137 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU L 184 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 151 through 153 removed outlier: 3.625A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR I 122 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER I 99 " --> pdb=" O SER I 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 33 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR I 122 " --> pdb=" O TYR I 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL I 196 " --> pdb=" O HIS I 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS I 179 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 209 through 215 removed outlier: 4.597A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.881A pdb=" N PHE M 76 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR M 77 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 41 through 43 removed outlier: 3.652A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 119 through 123 removed outlier: 3.938A pdb=" N PHE M 123 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL M 137 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU M 184 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS M 139 " --> pdb=" O SER M 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER M 182 " --> pdb=" O CYS M 139 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 151 through 153 removed outlier: 3.625A pdb=" N GLN M 152 " --> pdb=" O GLU M 200 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 212 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR J 122 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER J 99 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER J 33 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR J 122 " --> pdb=" O TYR J 94 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL J 196 " --> pdb=" O HIS J 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS J 179 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 209 through 215 removed outlier: 4.596A pdb=" N TYR J 209 " --> pdb=" O VAL J 226 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.881A pdb=" N PHE N 76 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR N 77 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 41 through 43 removed outlier: 3.652A pdb=" N GLY N 89 " --> pdb=" O VAL N 109 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 119 through 123 removed outlier: 3.938A pdb=" N PHE N 123 " --> pdb=" O VAL N 138 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL N 138 " --> pdb=" O PHE N 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL N 137 " --> pdb=" O LEU N 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU N 184 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS N 139 " --> pdb=" O SER N 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER N 182 " --> pdb=" O CYS N 139 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 151 through 153 removed outlier: 3.624A pdb=" N GLN N 152 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS N 212 " --> pdb=" O CYS N 199 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2868 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: 8.74 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10525 1.33 - 1.46: 10139 1.46 - 1.59: 15910 1.59 - 1.73: 0 1.73 - 1.86: 209 Bond restraints: 36783 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C LEU B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.330 1.390 -0.060 1.22e-02 6.72e+03 2.42e+01 bond pdb=" C GLU I 227 " pdb=" N PRO I 228 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.16e+01 bond pdb=" C GLN C 498 " pdb=" N PRO C 499 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.16e+01 bond pdb=" C GLU J 227 " pdb=" N PRO J 228 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.13e+01 ... (remaining 36778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 48071 2.74 - 5.47: 1656 5.47 - 8.21: 244 8.21 - 10.94: 47 10.94 - 13.68: 31 Bond angle restraints: 50049 Sorted by residual: angle pdb=" N SER J 145 " pdb=" CA SER J 145 " pdb=" C SER J 145 " ideal model delta sigma weight residual 111.36 102.86 8.50 1.09e+00 8.42e-01 6.08e+01 angle pdb=" N SER H 145 " pdb=" CA SER H 145 " pdb=" C SER H 145 " ideal model delta sigma weight residual 111.36 102.87 8.49 1.09e+00 8.42e-01 6.06e+01 angle pdb=" N SER I 145 " pdb=" CA SER I 145 " pdb=" C SER I 145 " ideal model delta sigma weight residual 111.36 102.88 8.48 1.09e+00 8.42e-01 6.05e+01 angle pdb=" CA GLN A1142 " pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 120.58 115.66 4.92 7.40e-01 1.83e+00 4.42e+01 angle pdb=" N THR B 274 " pdb=" CA THR B 274 " pdb=" C THR B 274 " ideal model delta sigma weight residual 108.32 97.60 10.72 1.64e+00 3.72e-01 4.27e+01 ... (remaining 50044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 20691 20.71 - 41.41: 1875 41.41 - 62.12: 457 62.12 - 82.82: 64 82.82 - 103.53: 31 Dihedral angle restraints: 23118 sinusoidal: 10107 harmonic: 13011 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 14.92 78.08 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 167.35 -74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.54 71.54 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 23115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 5893 0.267 - 0.535: 34 0.535 - 0.802: 2 0.802 - 1.069: 7 1.069 - 1.336: 4 Chirality restraints: 5940 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.46e+01 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.46e+01 ... (remaining 5937 not shown) Planarity restraints: 6392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.144 2.00e-02 2.50e+03 2.03e-01 5.13e+02 pdb=" CG ASN A 801 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.354 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " -0.032 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" CG ASN A 17 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " 0.335 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " -0.032 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" CG ASN B 17 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " 0.334 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " -0.216 2.00e-02 2.50e+03 ... (remaining 6389 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 511 2.50 - 3.10: 25874 3.10 - 3.70: 51910 3.70 - 4.30: 74353 4.30 - 4.90: 124828 Nonbonded interactions: 277476 Sorted by model distance: nonbonded pdb=" O VAL L 210 " pdb=" OG1 THR L 211 " model vdw 1.905 3.040 nonbonded pdb=" O VAL M 210 " pdb=" OG1 THR M 211 " model vdw 1.905 3.040 nonbonded pdb=" O VAL N 210 " pdb=" OG1 THR N 211 " model vdw 1.905 3.040 nonbonded pdb=" O ASP B 427 " pdb=" O ASP B 428 " model vdw 1.925 3.040 nonbonded pdb=" O SER M 10 " pdb=" OG SER M 11 " model vdw 1.930 3.040 ... (remaining 277471 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 14 through 441 or resid 449 or resid 451 through 452 or re \ sid 454 through 498 or resid 503 through 620 or resid 641 through 827 or resid 8 \ 53 through 1418)) selection = (chain 'B' and (resid 14 through 441 or resid 449 or resid 451 through 452 or re \ sid 454 or resid 491 through 620 or resid 641 through 675 or resid 690 through 1 \ 418)) selection = (chain 'C' and (resid 14 through 441 or resid 451 or resid 453 or resid 455 or r \ esid 457 or resid 491 through 498 or resid 503 through 827 or resid 853 through \ 1418)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'S' selection = chain 'T' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.560 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 32.690 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.012 0.733 36923 Z= 0.581 Angle : 1.580 56.662 50418 Z= 0.805 Chirality : 0.085 1.336 5940 Planarity : 0.009 0.177 6338 Dihedral : 16.708 103.530 14603 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 38.55 Ramachandran Plot: Outliers : 4.39 % Allowed : 13.18 % Favored : 82.43 % Rotamer: Outliers : 6.37 % Allowed : 12.36 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.10), residues: 4423 helix: -4.36 (0.10), residues: 623 sheet: -2.02 (0.15), residues: 1124 loop : -3.67 (0.09), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1107 TYR 0.027 0.002 TYR A1067 PHE 0.027 0.003 PHE B 238 TRP 0.044 0.003 TRP B 886 HIS 0.019 0.003 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.01125 (36783) covalent geometry : angle 1.23735 (50049) SS BOND : bond 0.12311 ( 51) SS BOND : angle 15.95369 ( 102) hydrogen bonds : bond 0.29479 ( 1033) hydrogen bonds : angle 10.25010 ( 2868) link_BETA1-4 : bond 0.01251 ( 35) link_BETA1-4 : angle 6.61408 ( 105) link_NAG-ASN : bond 0.05823 ( 54) link_NAG-ASN : angle 10.76138 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 412 time to evaluate : 1.078 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: A 16 VAL cc_start: 0.6604 (m) cc_final: 0.6381 (m) REVERT: A 811 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5324 (ttmm) REVERT: B 22 THR cc_start: 0.3373 (OUTLIER) cc_final: 0.2247 (t) REVERT: B 44 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7712 (mtt90) REVERT: B 173 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7168 (tm-30) REVERT: B 457 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.2757 (mmp80) REVERT: B 508 TYR cc_start: 0.7434 (m-80) cc_final: 0.7057 (m-80) REVERT: B 1142 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7466 (tp-100) REVERT: B 1146 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5639 (m-30) REVERT: C 418 ILE cc_start: 0.9122 (mt) cc_final: 0.8868 (tt) REVERT: C 720 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8688 (pt) REVERT: H 144 LYS cc_start: 0.3397 (mtmm) cc_final: 0.2914 (pttt) REVERT: L 12 PRO cc_start: 0.3224 (Cg_exo) cc_final: 0.2971 (Cg_endo) REVERT: I 57 GLU cc_start: 0.3524 (OUTLIER) cc_final: 0.2883 (pm20) REVERT: I 179 HIS cc_start: 0.1767 (OUTLIER) cc_final: 0.0092 (m170) REVERT: M 130 LEU cc_start: 0.1780 (mt) cc_final: 0.1321 (mm) REVERT: M 141 LEU cc_start: 0.3022 (mt) cc_final: 0.2803 (tp) REVERT: M 192 GLU cc_start: 0.2077 (OUTLIER) cc_final: 0.1363 (pt0) REVERT: J 18 VAL cc_start: -0.0933 (p) cc_final: -0.1321 (p) REVERT: J 185 LEU cc_start: 0.3015 (mt) cc_final: 0.2661 (tp) REVERT: J 229 LYS cc_start: 0.0594 (mtpm) cc_final: -0.0187 (pttp) REVERT: N 9 LEU cc_start: 0.0707 (OUTLIER) cc_final: 0.0103 (mt) REVERT: N 112 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4699 (tmtt) REVERT: N 192 GLU cc_start: 0.1154 (OUTLIER) cc_final: 0.0824 (mt-10) outliers start: 249 outliers final: 70 residues processed: 627 average time/residue: 0.2258 time to fit residues: 228.8361 Evaluate side-chains 309 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 226 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 179 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain N residue 144 PHE Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 195 LYS Chi-restraints excluded: chain N residue 203 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 414 GLN A 506 GLN A 658 ASN A 751 ASN A 755 GLN A 764 ASN A 804 GLN A 914 ASN A 969 ASN A 978 ASN A1142 GLN B 52 GLN B 121 ASN B 188 ASN B 271 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 498 GLN B 519 HIS B 544 ASN B 607 GLN B 644 GLN B 762 GLN B 901 GLN B 926 GLN B 957 GLN B1054 GLN B1101 HIS B1113 GLN C 121 ASN C 188 ASN C 321 GLN C 370 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN C 919 ASN C 949 GLN C1010 GLN C1101 HIS H 219 ASN L 43 GLN L 105 GLN L 160 GLN I 170 ASN I 219 ASN M 43 GLN M 105 GLN M 160 GLN M 204 GLN J 219 ASN N 6 GLN N 43 GLN N 157 ASN N 160 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.179958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.138180 restraints weight = 71554.846| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 4.03 r_work: 0.3118 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36923 Z= 0.202 Angle : 0.950 26.959 50418 Z= 0.454 Chirality : 0.055 0.660 5940 Planarity : 0.007 0.070 6338 Dihedral : 10.580 85.758 6822 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 1.15 % Allowed : 10.26 % Favored : 88.58 % Rotamer: Outliers : 4.61 % Allowed : 16.07 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.69 (0.11), residues: 4423 helix: -2.10 (0.17), residues: 663 sheet: -1.39 (0.16), residues: 1067 loop : -3.16 (0.10), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.024 0.002 TYR B 449 PHE 0.033 0.002 PHE M 144 TRP 0.023 0.002 TRP H 47 HIS 0.013 0.001 HIS J 179 Details of bonding type rmsd covalent geometry : bond 0.00456 (36783) covalent geometry : angle 0.88283 (50049) SS BOND : bond 0.00588 ( 51) SS BOND : angle 2.12002 ( 102) hydrogen bonds : bond 0.05767 ( 1033) hydrogen bonds : angle 6.45935 ( 2868) link_BETA1-4 : bond 0.01049 ( 35) link_BETA1-4 : angle 3.09043 ( 105) link_NAG-ASN : bond 0.00788 ( 54) link_NAG-ASN : angle 5.56961 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 272 time to evaluate : 1.312 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 23 GLN cc_start: 0.5048 (OUTLIER) cc_final: 0.4264 (mm-40) REVERT: A 353 TRP cc_start: 0.3175 (OUTLIER) cc_final: 0.2774 (p90) REVERT: A 495 TYR cc_start: 0.4311 (OUTLIER) cc_final: 0.2958 (m-80) REVERT: B 121 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7080 (t0) REVERT: B 152 TRP cc_start: 0.5301 (m100) cc_final: 0.4984 (m100) REVERT: B 173 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7317 (tm-30) REVERT: B 558 LYS cc_start: 0.7758 (pttt) cc_final: 0.7308 (mmtt) REVERT: C 22 THR cc_start: 0.1874 (OUTLIER) cc_final: 0.1606 (m) REVERT: C 24 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5368 (tt) REVERT: C 595 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.9199 (t) REVERT: H 169 TRP cc_start: -0.2888 (OUTLIER) cc_final: -0.3746 (t-100) REVERT: H 185 LEU cc_start: 0.2757 (mt) cc_final: 0.2508 (tt) REVERT: L 144 PHE cc_start: 0.2376 (OUTLIER) cc_final: 0.1196 (t80) REVERT: I 48 MET cc_start: 0.3689 (pmm) cc_final: 0.3470 (pmm) REVERT: I 115 MET cc_start: 0.4967 (mpp) cc_final: 0.4364 (mmt) REVERT: M 95 GLN cc_start: 0.2958 (pp30) cc_final: 0.1956 (pm20) REVERT: M 144 PHE cc_start: 0.0550 (OUTLIER) cc_final: -0.0200 (t80) REVERT: M 192 GLU cc_start: 0.1999 (OUTLIER) cc_final: 0.1201 (pt0) REVERT: J 18 VAL cc_start: 0.0688 (p) cc_final: 0.0386 (p) REVERT: N 8 PRO cc_start: 0.3209 (Cg_endo) cc_final: 0.2997 (Cg_exo) outliers start: 180 outliers final: 85 residues processed: 428 average time/residue: 0.1911 time to fit residues: 141.1616 Evaluate side-chains 323 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 227 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 144 PHE Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 203 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 105 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 205 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 542 ASN A 872 GLN A 954 GLN A 965 GLN B 14 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 506 GLN C 901 GLN C 955 ASN N 6 GLN N 58 ASN N 152 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.179049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.140745 restraints weight = 71061.571| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.79 r_work: 0.3131 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36923 Z= 0.198 Angle : 0.861 23.000 50418 Z= 0.406 Chirality : 0.051 0.609 5940 Planarity : 0.006 0.084 6338 Dihedral : 9.447 65.019 6741 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.15 % Favored : 89.06 % Rotamer: Outliers : 4.63 % Allowed : 17.38 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.07 (0.11), residues: 4423 helix: -0.74 (0.20), residues: 663 sheet: -1.05 (0.16), residues: 1060 loop : -2.97 (0.10), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 457 TYR 0.023 0.002 TYR B 170 PHE 0.019 0.002 PHE B 135 TRP 0.022 0.002 TRP J 169 HIS 0.012 0.001 HIS M 203 Details of bonding type rmsd covalent geometry : bond 0.00462 (36783) covalent geometry : angle 0.79554 (50049) SS BOND : bond 0.00598 ( 51) SS BOND : angle 2.21505 ( 102) hydrogen bonds : bond 0.05436 ( 1033) hydrogen bonds : angle 6.04758 ( 2868) link_BETA1-4 : bond 0.00744 ( 35) link_BETA1-4 : angle 3.07356 ( 105) link_NAG-ASN : bond 0.00763 ( 54) link_NAG-ASN : angle 5.10478 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 238 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.4897 (OUTLIER) cc_final: 0.4431 (mm110) REVERT: A 148 ASN cc_start: 0.6707 (m110) cc_final: 0.6458 (t0) REVERT: A 353 TRP cc_start: 0.3601 (OUTLIER) cc_final: 0.3345 (p90) REVERT: A 495 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.3106 (m-80) REVERT: B 40 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8161 (m-30) REVERT: B 152 TRP cc_start: 0.5401 (m100) cc_final: 0.4947 (m100) REVERT: B 173 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7173 (tm-30) REVERT: B 276 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7970 (tp) REVERT: B 558 LYS cc_start: 0.7936 (pttt) cc_final: 0.7498 (mmtt) REVERT: C 18 LEU cc_start: 0.4290 (OUTLIER) cc_final: 0.3610 (pp) REVERT: C 377 PHE cc_start: 0.8268 (t80) cc_final: 0.8039 (t80) REVERT: C 396 TYR cc_start: 0.8215 (m-80) cc_final: 0.7968 (m-80) REVERT: C 421 TYR cc_start: 0.8547 (m-10) cc_final: 0.8198 (m-10) REVERT: C 873 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: H 115 MET cc_start: 0.3908 (mmt) cc_final: 0.3224 (tpp) REVERT: H 169 TRP cc_start: -0.2658 (OUTLIER) cc_final: -0.3732 (t-100) REVERT: I 113 TYR cc_start: 0.2481 (m-10) cc_final: 0.2159 (m-10) REVERT: I 115 MET cc_start: 0.5012 (mpp) cc_final: 0.4552 (mpp) REVERT: I 169 TRP cc_start: -0.2308 (OUTLIER) cc_final: -0.2600 (t-100) REVERT: M 95 GLN cc_start: 0.2261 (pp30) cc_final: 0.1725 (pm20) REVERT: M 144 PHE cc_start: -0.0119 (OUTLIER) cc_final: -0.0832 (t80) REVERT: M 179 SER cc_start: -0.0743 (OUTLIER) cc_final: -0.1767 (t) REVERT: M 192 GLU cc_start: 0.2039 (OUTLIER) cc_final: 0.1291 (pt0) REVERT: J 18 VAL cc_start: 0.0410 (p) cc_final: 0.0056 (p) REVERT: J 52 ASP cc_start: 0.6523 (t0) cc_final: 0.6148 (t0) REVERT: N 97 THR cc_start: 0.1608 (OUTLIER) cc_final: 0.1299 (m) REVERT: N 203 HIS cc_start: 0.0741 (OUTLIER) cc_final: 0.0413 (p-80) outliers start: 181 outliers final: 98 residues processed: 392 average time/residue: 0.1886 time to fit residues: 127.4988 Evaluate side-chains 324 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 212 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 179 SER Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 203 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 125 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 423 optimal weight: 0.0970 chunk 44 optimal weight: 30.0000 chunk 424 optimal weight: 0.0030 chunk 162 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 418 optimal weight: 20.0000 chunk 296 optimal weight: 3.9990 chunk 429 optimal weight: 2.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN L 171 GLN M 42 GLN N 6 GLN ** N 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.180545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141243 restraints weight = 71018.738| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.77 r_work: 0.3160 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36923 Z= 0.145 Angle : 0.798 21.781 50418 Z= 0.373 Chirality : 0.049 0.500 5940 Planarity : 0.005 0.081 6338 Dihedral : 8.558 67.467 6721 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.18 % Favored : 90.14 % Rotamer: Outliers : 3.61 % Allowed : 19.15 % Favored : 77.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.68 (0.12), residues: 4423 helix: -0.04 (0.21), residues: 661 sheet: -0.99 (0.16), residues: 1026 loop : -2.71 (0.10), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 457 TYR 0.030 0.001 TYR B 453 PHE 0.023 0.001 PHE L 99 TRP 0.011 0.001 TRP I 47 HIS 0.009 0.001 HIS M 203 Details of bonding type rmsd covalent geometry : bond 0.00329 (36783) covalent geometry : angle 0.74020 (50049) SS BOND : bond 0.00524 ( 51) SS BOND : angle 1.73349 ( 102) hydrogen bonds : bond 0.04452 ( 1033) hydrogen bonds : angle 5.72498 ( 2868) link_BETA1-4 : bond 0.00711 ( 35) link_BETA1-4 : angle 2.88434 ( 105) link_NAG-ASN : bond 0.00596 ( 54) link_NAG-ASN : angle 4.64874 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 242 time to evaluate : 1.291 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 168 PHE cc_start: 0.8197 (t80) cc_final: 0.7884 (t80) REVERT: A 495 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.3067 (m-80) REVERT: A 814 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: A 900 MET cc_start: 0.9136 (mtp) cc_final: 0.8932 (mtm) REVERT: B 40 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: B 78 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4739 (mmp80) REVERT: B 173 GLN cc_start: 0.7991 (mm-40) cc_final: 0.6963 (tm-30) REVERT: B 558 LYS cc_start: 0.7959 (pttt) cc_final: 0.7504 (mmtt) REVERT: C 396 TYR cc_start: 0.8098 (m-80) cc_final: 0.7656 (m-80) REVERT: C 421 TYR cc_start: 0.8451 (m-10) cc_final: 0.8221 (m-10) REVERT: C 457 ARG cc_start: 0.7043 (mpt90) cc_final: 0.6547 (mpt90) REVERT: C 873 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: H 80 TYR cc_start: 0.5594 (m-80) cc_final: 0.4831 (m-10) REVERT: H 169 TRP cc_start: -0.2774 (OUTLIER) cc_final: -0.3642 (t-100) REVERT: L 144 PHE cc_start: 0.2217 (OUTLIER) cc_final: 0.0600 (t80) REVERT: I 34 MET cc_start: 0.1483 (OUTLIER) cc_final: 0.1207 (mtt) REVERT: I 70 MET cc_start: 0.3629 (tpp) cc_final: 0.3076 (tpp) REVERT: I 113 TYR cc_start: 0.2387 (m-10) cc_final: 0.2068 (m-10) REVERT: I 115 MET cc_start: 0.4959 (mpp) cc_final: 0.4526 (mmt) REVERT: M 95 GLN cc_start: 0.2064 (pp30) cc_final: 0.1550 (pm20) REVERT: M 144 PHE cc_start: -0.0095 (OUTLIER) cc_final: -0.0941 (t80) REVERT: M 192 GLU cc_start: 0.1646 (OUTLIER) cc_final: 0.1301 (pt0) REVERT: J 18 VAL cc_start: 0.0464 (p) cc_final: 0.0167 (p) REVERT: J 31 GLU cc_start: 0.6663 (pt0) cc_final: 0.6283 (tp30) REVERT: J 34 MET cc_start: 0.3539 (tpp) cc_final: 0.3035 (pmm) REVERT: J 46 GLU cc_start: 0.5753 (tp30) cc_final: 0.5428 (pm20) REVERT: J 168 SER cc_start: 0.4847 (m) cc_final: 0.4624 (p) REVERT: N 148 GLU cc_start: -0.1761 (OUTLIER) cc_final: -0.2082 (pt0) outliers start: 141 outliers final: 87 residues processed: 362 average time/residue: 0.1856 time to fit residues: 116.8577 Evaluate side-chains 309 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 211 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 336 optimal weight: 30.0000 chunk 342 optimal weight: 3.9990 chunk 429 optimal weight: 40.0000 chunk 266 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 425 optimal weight: 0.2980 chunk 280 optimal weight: 2.9990 chunk 393 optimal weight: 30.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 762 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN L 6 GLN N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.179384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.140377 restraints weight = 70863.145| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.72 r_work: 0.3144 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36923 Z= 0.178 Angle : 0.800 21.366 50418 Z= 0.374 Chirality : 0.049 0.457 5940 Planarity : 0.005 0.076 6338 Dihedral : 8.205 68.881 6704 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.54 % Favored : 89.89 % Rotamer: Outliers : 4.25 % Allowed : 19.53 % Favored : 76.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.53 (0.12), residues: 4423 helix: 0.11 (0.21), residues: 664 sheet: -0.87 (0.15), residues: 1087 loop : -2.65 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.022 0.001 TYR C1067 PHE 0.018 0.001 PHE B 106 TRP 0.020 0.002 TRP A 258 HIS 0.008 0.001 HIS M 203 Details of bonding type rmsd covalent geometry : bond 0.00422 (36783) covalent geometry : angle 0.74359 (50049) SS BOND : bond 0.00578 ( 51) SS BOND : angle 1.72271 ( 102) hydrogen bonds : bond 0.04764 ( 1033) hydrogen bonds : angle 5.63004 ( 2868) link_BETA1-4 : bond 0.00629 ( 35) link_BETA1-4 : angle 2.86994 ( 105) link_NAG-ASN : bond 0.00625 ( 54) link_NAG-ASN : angle 4.58373 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 224 time to evaluate : 1.279 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 69 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.5597 (t70) REVERT: A 495 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.2813 (m-10) REVERT: A 814 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8838 (mtmm) REVERT: B 40 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: B 41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8573 (mmtp) REVERT: B 78 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.4833 (mmp80) REVERT: B 154 GLU cc_start: 0.7902 (mp0) cc_final: 0.7682 (mp0) REVERT: B 173 GLN cc_start: 0.7918 (mm-40) cc_final: 0.6913 (tm-30) REVERT: B 188 ASN cc_start: 0.7088 (m110) cc_final: 0.6795 (t0) REVERT: B 558 LYS cc_start: 0.7811 (pttt) cc_final: 0.7507 (mmtt) REVERT: C 396 TYR cc_start: 0.8059 (m-80) cc_final: 0.7565 (m-80) REVERT: C 457 ARG cc_start: 0.6898 (mpt90) cc_final: 0.5808 (tmm-80) REVERT: C 873 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: H 27 TYR cc_start: 0.6735 (m-80) cc_final: 0.6480 (m-80) REVERT: H 80 TYR cc_start: 0.5642 (m-80) cc_final: 0.5050 (m-10) REVERT: H 81 MET cc_start: 0.2343 (tmm) cc_final: 0.1982 (tmm) REVERT: H 115 MET cc_start: 0.4235 (mmt) cc_final: 0.3675 (tpp) REVERT: H 198 THR cc_start: -0.0213 (OUTLIER) cc_final: -0.0421 (p) REVERT: L 6 GLN cc_start: 0.3401 (OUTLIER) cc_final: 0.2653 (mp10) REVERT: I 34 MET cc_start: 0.1534 (OUTLIER) cc_final: 0.1245 (mtt) REVERT: I 70 MET cc_start: 0.3672 (tpp) cc_final: 0.3022 (tpp) REVERT: I 115 MET cc_start: 0.4608 (mpp) cc_final: 0.4142 (mmt) REVERT: M 95 GLN cc_start: 0.2161 (pp30) cc_final: 0.1646 (pm20) REVERT: M 144 PHE cc_start: 0.0302 (OUTLIER) cc_final: -0.0654 (t80) REVERT: M 192 GLU cc_start: 0.1378 (OUTLIER) cc_final: 0.0963 (pt0) REVERT: J 18 VAL cc_start: 0.0383 (p) cc_final: 0.0038 (p) REVERT: J 34 MET cc_start: 0.3500 (tpp) cc_final: 0.3188 (pmm) outliers start: 166 outliers final: 115 residues processed: 370 average time/residue: 0.1874 time to fit residues: 120.5798 Evaluate side-chains 332 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 205 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 309 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 chunk 344 optimal weight: 30.0000 chunk 435 optimal weight: 20.0000 chunk 102 optimal weight: 0.0470 chunk 187 optimal weight: 1.9990 chunk 428 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 268 optimal weight: 7.9990 chunk 422 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 422 ASN C 901 GLN I 179 HIS N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.181105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.142434 restraints weight = 71079.682| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.65 r_work: 0.3165 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36923 Z= 0.157 Angle : 0.775 21.280 50418 Z= 0.362 Chirality : 0.048 0.457 5940 Planarity : 0.005 0.072 6338 Dihedral : 7.975 59.928 6701 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.98 % Favored : 90.50 % Rotamer: Outliers : 3.74 % Allowed : 20.42 % Favored : 75.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.41 (0.12), residues: 4423 helix: 0.30 (0.21), residues: 662 sheet: -0.83 (0.15), residues: 1090 loop : -2.59 (0.11), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 454 TYR 0.020 0.001 TYR B 453 PHE 0.017 0.001 PHE L 99 TRP 0.026 0.001 TRP A 258 HIS 0.006 0.001 HIS M 203 Details of bonding type rmsd covalent geometry : bond 0.00367 (36783) covalent geometry : angle 0.71960 (50049) SS BOND : bond 0.00516 ( 51) SS BOND : angle 1.58816 ( 102) hydrogen bonds : bond 0.04409 ( 1033) hydrogen bonds : angle 5.49690 ( 2868) link_BETA1-4 : bond 0.00710 ( 35) link_BETA1-4 : angle 2.79361 ( 105) link_NAG-ASN : bond 0.00610 ( 54) link_NAG-ASN : angle 4.48179 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 223 time to evaluate : 1.351 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 69 HIS cc_start: 0.6638 (OUTLIER) cc_final: 0.5654 (t70) REVERT: A 79 PHE cc_start: 0.7154 (t80) cc_final: 0.6931 (t80) REVERT: A 495 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.4303 (m-10) REVERT: A 814 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8831 (mppt) REVERT: B 40 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 41 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8576 (mmtp) REVERT: B 78 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.4739 (mmp80) REVERT: B 153 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6014 (pmm) REVERT: B 188 ASN cc_start: 0.7008 (m110) cc_final: 0.6772 (t0) REVERT: B 237 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.6735 (mtp180) REVERT: B 558 LYS cc_start: 0.7935 (pttt) cc_final: 0.7514 (mmtt) REVERT: C 396 TYR cc_start: 0.8034 (m-80) cc_final: 0.7304 (m-80) REVERT: C 456 PHE cc_start: 0.7491 (m-80) cc_final: 0.6942 (m-80) REVERT: C 457 ARG cc_start: 0.6765 (mpt90) cc_final: 0.5850 (tmm-80) REVERT: C 584 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8144 (pt) REVERT: C 873 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: H 57 GLU cc_start: 0.6256 (pp20) cc_final: 0.6016 (pp20) REVERT: H 80 TYR cc_start: 0.5751 (m-80) cc_final: 0.5048 (m-10) REVERT: H 115 MET cc_start: 0.4301 (mmt) cc_final: 0.3699 (tpp) REVERT: L 144 PHE cc_start: 0.2533 (OUTLIER) cc_final: 0.0858 (t80) REVERT: I 70 MET cc_start: 0.3606 (tpp) cc_final: 0.2984 (tpp) REVERT: I 115 MET cc_start: 0.4681 (mpp) cc_final: 0.4242 (mmt) REVERT: M 95 GLN cc_start: 0.1968 (pp30) cc_final: 0.1654 (pm20) REVERT: M 144 PHE cc_start: 0.0182 (OUTLIER) cc_final: -0.0749 (t80) REVERT: J 18 VAL cc_start: 0.0385 (p) cc_final: 0.0036 (p) REVERT: J 34 MET cc_start: 0.3736 (tpp) cc_final: 0.3486 (pmm) REVERT: J 112 TYR cc_start: 0.2693 (t80) cc_final: 0.2016 (t80) REVERT: N 4 MET cc_start: 0.1662 (ptm) cc_final: 0.1298 (ptm) outliers start: 146 outliers final: 105 residues processed: 347 average time/residue: 0.1827 time to fit residues: 109.6845 Evaluate side-chains 327 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 211 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 367 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 chunk 349 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN M 165 GLN N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.179852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.140528 restraints weight = 71189.844| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.77 r_work: 0.3135 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36923 Z= 0.204 Angle : 0.800 20.950 50418 Z= 0.374 Chirality : 0.050 0.486 5940 Planarity : 0.005 0.074 6338 Dihedral : 8.050 59.877 6697 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.72 % Favored : 89.85 % Rotamer: Outliers : 4.17 % Allowed : 20.35 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.39 (0.12), residues: 4423 helix: 0.27 (0.21), residues: 657 sheet: -0.88 (0.15), residues: 1104 loop : -2.52 (0.11), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.021 0.001 TYR B 453 PHE 0.019 0.002 PHE B 106 TRP 0.017 0.002 TRP A 258 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00488 (36783) covalent geometry : angle 0.74535 (50049) SS BOND : bond 0.01111 ( 51) SS BOND : angle 1.78004 ( 102) hydrogen bonds : bond 0.04940 ( 1033) hydrogen bonds : angle 5.59070 ( 2868) link_BETA1-4 : bond 0.00706 ( 35) link_BETA1-4 : angle 2.83957 ( 105) link_NAG-ASN : bond 0.00622 ( 54) link_NAG-ASN : angle 4.49800 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 234 time to evaluate : 1.334 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 69 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.5455 (t70) REVERT: A 361 CYS cc_start: 0.2641 (OUTLIER) cc_final: 0.2371 (p) REVERT: A 814 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8784 (mtmm) REVERT: B 40 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: B 41 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8582 (mmtp) REVERT: B 78 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.4673 (mmp80) REVERT: B 153 MET cc_start: 0.6495 (ptm) cc_final: 0.6022 (pmm) REVERT: B 173 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7029 (tm-30) REVERT: B 188 ASN cc_start: 0.7233 (m110) cc_final: 0.6911 (t0) REVERT: B 273 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: B 558 LYS cc_start: 0.7879 (pttt) cc_final: 0.7435 (mmtt) REVERT: C 456 PHE cc_start: 0.7658 (m-80) cc_final: 0.7088 (m-80) REVERT: C 457 ARG cc_start: 0.6780 (mpt90) cc_final: 0.5868 (tmm-80) REVERT: C 584 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (pt) REVERT: C 873 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: H 80 TYR cc_start: 0.5707 (m-80) cc_final: 0.5029 (m-10) REVERT: H 115 MET cc_start: 0.4393 (mmt) cc_final: 0.3617 (tpp) REVERT: L 144 PHE cc_start: 0.2690 (OUTLIER) cc_final: 0.0812 (t80) REVERT: I 115 MET cc_start: 0.4481 (mpp) cc_final: 0.4089 (mmt) REVERT: I 190 LEU cc_start: 0.2130 (tp) cc_final: 0.1710 (pp) REVERT: M 95 GLN cc_start: 0.2285 (pp30) cc_final: 0.1821 (pm20) REVERT: M 144 PHE cc_start: 0.0150 (OUTLIER) cc_final: -0.0868 (t80) REVERT: J 34 MET cc_start: 0.3811 (tpp) cc_final: 0.3304 (pmm) REVERT: J 112 TYR cc_start: 0.2853 (t80) cc_final: 0.2265 (t80) REVERT: J 169 TRP cc_start: -0.0858 (OUTLIER) cc_final: -0.1503 (m-90) outliers start: 163 outliers final: 122 residues processed: 376 average time/residue: 0.1923 time to fit residues: 124.2701 Evaluate side-chains 346 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 212 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 424 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 418 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 386 optimal weight: 8.9990 chunk 312 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 644 GLN B 394 ASN B 506 GLN B 901 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN M 165 GLN ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.174729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134705 restraints weight = 70764.960| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.83 r_work: 0.3093 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.007 0.073 36923 Z= 0.272 Angle : 0.844 20.854 50418 Z= 0.396 Chirality : 0.052 0.510 5940 Planarity : 0.005 0.074 6338 Dihedral : 8.354 59.783 6694 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.24 % Favored : 89.31 % Rotamer: Outliers : 4.02 % Allowed : 20.89 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.49 (0.12), residues: 4423 helix: -0.00 (0.21), residues: 660 sheet: -0.92 (0.15), residues: 1204 loop : -2.61 (0.11), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 408 TYR 0.022 0.002 TYR C1067 PHE 0.018 0.002 PHE C 429 TRP 0.014 0.002 TRP A 258 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00662 (36783) covalent geometry : angle 0.78955 (50049) SS BOND : bond 0.00750 ( 51) SS BOND : angle 2.00798 ( 102) hydrogen bonds : bond 0.05431 ( 1033) hydrogen bonds : angle 5.70500 ( 2868) link_BETA1-4 : bond 0.00673 ( 35) link_BETA1-4 : angle 2.91636 ( 105) link_NAG-ASN : bond 0.00650 ( 54) link_NAG-ASN : angle 4.56205 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 212 time to evaluate : 0.967 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 69 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5478 (t70) REVERT: A 619 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: A 814 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8911 (mtmm) REVERT: B 40 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: B 41 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8518 (mmtp) REVERT: B 78 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4807 (mmp80) REVERT: B 153 MET cc_start: 0.6267 (ptm) cc_final: 0.5902 (pmm) REVERT: B 188 ASN cc_start: 0.7083 (m110) cc_final: 0.6775 (t0) REVERT: B 558 LYS cc_start: 0.7970 (pttt) cc_final: 0.7630 (mmtt) REVERT: C 242 LEU cc_start: 0.6968 (mm) cc_final: 0.6706 (mm) REVERT: C 506 GLN cc_start: 0.7712 (pt0) cc_final: 0.6996 (pt0) REVERT: C 873 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: H 115 MET cc_start: 0.4510 (mmt) cc_final: 0.3675 (tpp) REVERT: L 144 PHE cc_start: 0.2670 (OUTLIER) cc_final: 0.0898 (t80) REVERT: I 115 MET cc_start: 0.4401 (mpp) cc_final: 0.3999 (mmt) REVERT: M 95 GLN cc_start: 0.2257 (pp30) cc_final: 0.1083 (pt0) REVERT: M 144 PHE cc_start: 0.0330 (OUTLIER) cc_final: -0.0793 (t80) REVERT: M 168 VAL cc_start: 0.4286 (t) cc_final: 0.3855 (p) REVERT: J 34 MET cc_start: 0.3944 (tpp) cc_final: 0.3519 (pmm) REVERT: J 112 TYR cc_start: 0.3266 (t80) cc_final: 0.2633 (t80) REVERT: J 169 TRP cc_start: -0.0782 (OUTLIER) cc_final: -0.1421 (m-90) outliers start: 157 outliers final: 124 residues processed: 349 average time/residue: 0.1919 time to fit residues: 115.5780 Evaluate side-chains 336 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 202 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 191 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 245 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN H 39 GLN M 165 GLN M 171 GLN ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 129 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 = 0.4437 r_free = 0.4437 target = 0.179464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140567 restraints weight = 70966.984| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.73 r_work: 0.3137 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36923 Z= 0.180 Angle : 0.785 20.877 50418 Z= 0.367 Chirality : 0.049 0.492 5940 Planarity : 0.005 0.071 6338 Dihedral : 8.059 59.554 6693 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.36 % Favored : 90.21 % Rotamer: Outliers : 3.76 % Allowed : 21.24 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.33 (0.12), residues: 4423 helix: 0.21 (0.21), residues: 665 sheet: -0.83 (0.15), residues: 1171 loop : -2.51 (0.11), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE C 456 TRP 0.037 0.001 TRP A 258 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00428 (36783) covalent geometry : angle 0.73213 (50049) SS BOND : bond 0.00645 ( 51) SS BOND : angle 1.72043 ( 102) hydrogen bonds : bond 0.04636 ( 1033) hydrogen bonds : angle 5.52109 ( 2868) link_BETA1-4 : bond 0.00694 ( 35) link_BETA1-4 : angle 2.76295 ( 105) link_NAG-ASN : bond 0.00605 ( 54) link_NAG-ASN : angle 4.41676 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 209 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.5585 (t70) REVERT: A 220 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 814 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8879 (mtmm) REVERT: B 40 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: B 41 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8537 (mmtp) REVERT: B 78 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4669 (mmp80) REVERT: B 153 MET cc_start: 0.6114 (ptm) cc_final: 0.5884 (pmm) REVERT: B 188 ASN cc_start: 0.7137 (m110) cc_final: 0.6811 (t0) REVERT: B 273 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7010 (mtp180) REVERT: B 1141 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8274 (tt) REVERT: C 177 MET cc_start: 0.6315 (mmm) cc_final: 0.6021 (tmm) REVERT: C 242 LEU cc_start: 0.6877 (mm) cc_final: 0.6672 (mm) REVERT: C 456 PHE cc_start: 0.7604 (m-80) cc_final: 0.7378 (m-80) REVERT: C 873 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: H 80 TYR cc_start: 0.5487 (m-80) cc_final: 0.5032 (m-10) REVERT: H 115 MET cc_start: 0.4552 (mmt) cc_final: 0.3703 (tpp) REVERT: L 144 PHE cc_start: 0.2869 (OUTLIER) cc_final: 0.0984 (t80) REVERT: I 57 GLU cc_start: 0.3792 (OUTLIER) cc_final: 0.3488 (pm20) REVERT: I 115 MET cc_start: 0.4555 (mpp) cc_final: 0.4235 (mmt) REVERT: M 95 GLN cc_start: 0.1866 (pp30) cc_final: 0.0809 (pt0) REVERT: M 144 PHE cc_start: 0.0174 (OUTLIER) cc_final: -0.0948 (t80) REVERT: M 168 VAL cc_start: 0.4192 (t) cc_final: 0.3708 (p) REVERT: J 34 MET cc_start: 0.3996 (tpp) cc_final: 0.3569 (pmm) REVERT: J 112 TYR cc_start: 0.2711 (t80) cc_final: 0.2136 (t80) REVERT: J 144 LYS cc_start: 0.1197 (mtmm) cc_final: 0.0748 (tttt) REVERT: J 169 TRP cc_start: -0.0767 (OUTLIER) cc_final: -0.1423 (m-90) REVERT: N 4 MET cc_start: 0.1961 (ptm) cc_final: 0.1570 (ptt) outliers start: 147 outliers final: 113 residues processed: 336 average time/residue: 0.1918 time to fit residues: 111.2482 Evaluate side-chains 323 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 197 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 188 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 330 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 901 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.179839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140708 restraints weight = 70937.951| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.58 r_work: 0.3164 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36923 Z= 0.141 Angle : 0.762 20.685 50418 Z= 0.354 Chirality : 0.048 0.481 5940 Planarity : 0.005 0.074 6338 Dihedral : 7.794 59.671 6692 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.11 % Favored : 90.46 % Rotamer: Outliers : 3.12 % Allowed : 21.83 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.20 (0.12), residues: 4423 helix: 0.49 (0.21), residues: 665 sheet: -0.80 (0.15), residues: 1169 loop : -2.44 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 457 TYR 0.023 0.001 TYR C 170 PHE 0.024 0.001 PHE C 456 TRP 0.029 0.001 TRP A 258 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00325 (36783) covalent geometry : angle 0.70687 (50049) SS BOND : bond 0.00525 ( 51) SS BOND : angle 1.55973 ( 102) hydrogen bonds : bond 0.04201 ( 1033) hydrogen bonds : angle 5.38007 ( 2868) link_BETA1-4 : bond 0.00701 ( 35) link_BETA1-4 : angle 2.75278 ( 105) link_NAG-ASN : bond 0.00639 ( 54) link_NAG-ASN : angle 4.43950 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 203 time to evaluate : 1.373 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 69 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.5614 (t70) REVERT: A 220 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 40 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: B 78 ARG cc_start: 0.5233 (OUTLIER) cc_final: 0.4592 (mmp80) REVERT: B 188 ASN cc_start: 0.7107 (m110) cc_final: 0.6793 (t0) REVERT: B 273 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6948 (mtp180) REVERT: C 177 MET cc_start: 0.6365 (mmm) cc_final: 0.6110 (tmm) REVERT: C 242 LEU cc_start: 0.6848 (mm) cc_final: 0.6577 (mm) REVERT: C 584 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8167 (pt) REVERT: C 873 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: H 80 TYR cc_start: 0.5488 (m-80) cc_final: 0.5023 (m-10) REVERT: H 115 MET cc_start: 0.4672 (mmt) cc_final: 0.3821 (tpp) REVERT: L 4 MET cc_start: 0.3819 (mtt) cc_final: 0.2311 (ptm) REVERT: L 144 PHE cc_start: 0.2923 (OUTLIER) cc_final: 0.1031 (t80) REVERT: I 115 MET cc_start: 0.4533 (mpp) cc_final: 0.4208 (mmt) REVERT: M 95 GLN cc_start: 0.1799 (pp30) cc_final: 0.0839 (pt0) REVERT: M 144 PHE cc_start: 0.0302 (OUTLIER) cc_final: -0.0859 (t80) REVERT: M 168 VAL cc_start: 0.4174 (t) cc_final: 0.3744 (p) REVERT: J 34 MET cc_start: 0.3907 (tpp) cc_final: 0.3539 (pmm) REVERT: J 112 TYR cc_start: 0.2699 (t80) cc_final: 0.2167 (t80) REVERT: J 144 LYS cc_start: 0.1127 (mtmm) cc_final: 0.0700 (tttt) REVERT: J 169 TRP cc_start: -0.0876 (OUTLIER) cc_final: -0.1554 (m-90) REVERT: N 6 GLN cc_start: 0.2461 (OUTLIER) cc_final: 0.2023 (mt0) outliers start: 122 outliers final: 99 residues processed: 308 average time/residue: 0.1909 time to fit residues: 101.6412 Evaluate side-chains 306 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 196 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 44 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 382 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 431 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN C 901 GLN N 6 GLN ** N 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.180622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.141791 restraints weight = 70468.252| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 3.55 r_work: 0.3144 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36923 Z= 0.194 Angle : 0.788 20.522 50418 Z= 0.368 Chirality : 0.049 0.501 5940 Planarity : 0.005 0.071 6338 Dihedral : 7.807 59.712 6684 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.38 % Favored : 90.19 % Rotamer: Outliers : 3.22 % Allowed : 21.83 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.22 (0.12), residues: 4423 helix: 0.42 (0.21), residues: 665 sheet: -0.71 (0.15), residues: 1149 loop : -2.48 (0.11), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.021 0.001 TYR C1067 PHE 0.020 0.002 PHE B 106 TRP 0.026 0.001 TRP A 258 HIS 0.009 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00466 (36783) covalent geometry : angle 0.73529 (50049) SS BOND : bond 0.00590 ( 51) SS BOND : angle 1.70415 ( 102) hydrogen bonds : bond 0.04713 ( 1033) hydrogen bonds : angle 5.43392 ( 2868) link_BETA1-4 : bond 0.00696 ( 35) link_BETA1-4 : angle 2.77816 ( 105) link_NAG-ASN : bond 0.00628 ( 54) link_NAG-ASN : angle 4.42460 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12354.98 seconds wall clock time: 210 minutes 51.03 seconds (12651.03 seconds total)